Microbial Diversity and Environmental Adaptability of Microorganisms in Extreme Environments

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

Deadline for manuscript submissions: 30 June 2024 | Viewed by 4585

Special Issue Editors

1. Polar Research Institute of China, Shanghai 200240, China
2. School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
Interests: polar regions; marine microbiology; adaptation and evolution, diversity
College of Marine Life Sciences, Ocean University of China, Qingdao 266000, China
Interests: marine microbiology; biogeochemical cycles; organic sulfur cycling; catalytic mechanisms
State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266000, China
Interests: marine microorganisms; communities diversity; genomic evolution; adaptation
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Special Issue Information

Dear Colleagues,

Microorganisms, the simplest and most diverse biological group in the ecosystem, are ideal models for studying the survival, adaptation, and evolution of life. Although it is challenging for microorganisms to live in extreme environments, such as the polar regions, the deep sea, hydrothermal vents and hot springs, for example, their diversity, functions and survival strategies are impressive. Nevertheless, we have been trying to best understand the basic questions as to the diversity of microorganisms living in extreme environments, and how they survive and evolve under extreme conditions. With the development of multiomics and advanced cultivation approaches, it is possible to gain a much better understanding of microbial diversity and survival strategies in extreme environments.

The aim of this collection of articles is to provide an overview of the current knowledge on the diversity, survival and adaptation mechanisms of microorganisms in various extreme environments. Reviews and research related to culture-dependent and culture-independent studies of microbial diversity in extreme environments are encouraged. In-depth studies on the adaptation and survival mechanisms through genomics, transcriptomics, proteomics, biochemistry or structural biology are welcome. New methods and concepts for this research topic are encouraged. All article types are welcome.

Dr. Li Liao
Dr. Chunyang Li
Dr. Qilong Qin
Guest Editors

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Keywords

  • diversity
  • adaptation
  • mechanism
  • extreme environment
  • extremophile

Published Papers (4 papers)

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Research

14 pages, 3569 KiB  
Article
Integrated Analysis of the Intestinal Microbiota and Transcriptome of Fenneropenaeus chinensis Response to Low-Salinity Stress
Biology 2023, 12(12), 1502; https://doi.org/10.3390/biology12121502 - 07 Dec 2023
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Abstract
Salinity is an important environmental stress factor in mariculture. Shrimp intestines harbor dense and diverse microbial communities that maintain host health and anti-pathogen capabilities under salinity stress. In this study, 16s amplicon and transcriptome sequencing were used to analyze the intestine of Fenneropenaeus [...] Read more.
Salinity is an important environmental stress factor in mariculture. Shrimp intestines harbor dense and diverse microbial communities that maintain host health and anti-pathogen capabilities under salinity stress. In this study, 16s amplicon and transcriptome sequencing were used to analyze the intestine of Fenneropenaeus chinensis under low-salinity stress (15 ppt). This study aimed to investigate the response mechanisms of the intestinal microbiota and gene expression to acute low-salinity stress. The intestinal tissues of F. chinensis were analyzed using 16S microbiota and transcriptome sequencing. The microbiota analysis demonstrated that the relative abundances of Photobacterium and Vibrio decreased significantly, whereas Shewanella, Pseudomonas, Lactobacillus, Ralstonia, Colwellia, Cohaesibacter, Fusibacter, and Lachnospiraceae_NK4A136_group became the predominant communities. Transcriptome sequencing identified numerous differentially expressed genes (DEGs). The DEGs were clustered into many Gene Ontology terms and further enriched in some immunity- or metabolism-related Kyoto Encyclopedia of Genes and Genomes pathways, including various types of N-glycan biosynthesis, amino acid sugar and nucleotide sugar metabolism, and lysosome and fatty acid metabolism. Correlation analysis between microbiota and DEGs showed that changes in Pseudomonas, Ralstonia, Colwellia, and Cohaesibacter were positively correlated with immune-related genes such as peritrophin-1-like and mucin-2-like, and negatively correlated with caspase-1-like genes. Low-salinity stress caused changes in intestinal microorganisms and their gene expression, with a close correlation between them. Full article
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23 pages, 857 KiB  
Article
Shifts in the Microbial Populations of Bioleach Reactors Are Determined by Carbon Sources and Temperature
Biology 2023, 12(11), 1411; https://doi.org/10.3390/biology12111411 - 09 Nov 2023
Cited by 1 | Viewed by 985
Abstract
In the present study, the effect of additional carbon sources (carbon dioxide and molasses) on the bio-oxidation of a pyrite–arsenopyrite concentrate at temperatures of 40–50 °C was studied, and novel data regarding the patterns of the bio-oxidation of gold-bearing sulfide concentrates and the [...] Read more.
In the present study, the effect of additional carbon sources (carbon dioxide and molasses) on the bio-oxidation of a pyrite–arsenopyrite concentrate at temperatures of 40–50 °C was studied, and novel data regarding the patterns of the bio-oxidation of gold-bearing sulfide concentrates and the composition of the microbial populations performing these processes were obtained. At 40 °C, additional carbon sources did not affect the bio-oxidation efficiency. At the same time, the application of additional carbon dioxide improved the bio-oxidation performance at temperatures of 45 and 50 °C and made it possible to avoid the inhibition of bio-oxidation due to an increase in the temperature. Therefore, the use of additional carbon dioxide may be proposed to prevent the negative effect of an increase in temperature on the bio-oxidation of sulfide concentrates. 16S rRNA gene profiling revealed archaea of the family Thermoplasmataceae (Acidiplasma, Ferroplasma, Cuniculiplasma, and A-plasma group) and bacteria of the genera Leptospirillum, with Sulfobacillus and Acidithiobacillus among the dominant groups in the community. Temperature influenced the composition of the communities to a greater extent than the additional sources of carbon and the mode of operation of the bioreactor. Elevating the temperature from 40 °C to 50 °C resulted in increases in the shares of Acidiplasma and Sulfobacillus and decreases in the relative abundances of Ferroplasma, Leptospirillum, and Acidithiobacillus, while Cuniculiplasma and A-plasma were more abundant at 45 °C. A metagenomic analysis of the studied population made it possible to characterize novel archaea belonging to an uncultivated, poorly-studied group of Thermoplasmatales which potentially plays an important role in the bio-oxidation process. Based on an analysis of the complete genome, we propose describing the novel species and novel genus as “Candidatus Carboxiplasma ferriphilum” gen. nov., spec. nov. Full article
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18 pages, 4000 KiB  
Article
Harnessing Diesel-Degrading Potential of an Antarctic Microalga from Greenwich Island and Its Physiological Adaptation
Biology 2023, 12(8), 1142; https://doi.org/10.3390/biology12081142 - 17 Aug 2023
Viewed by 1318
Abstract
Microalgae are well known for their metal sorption capacities, but their potential in the remediation of hydrophobic organic compounds has received little attention in polar regions. We evaluated in the laboratory the ability of an Antarctic microalga to remediate diesel hydrocarbons and also [...] Read more.
Microalgae are well known for their metal sorption capacities, but their potential in the remediation of hydrophobic organic compounds has received little attention in polar regions. We evaluated in the laboratory the ability of an Antarctic microalga to remediate diesel hydrocarbons and also investigated physiological changes consequent upon diesel exposure. Using a polyphasic taxonomic approach, the microalgal isolate, WCY_AQ5_1, originally sampled from Greenwich Island (South Shetland Islands, maritime Antarctica) was identified as Tritostichococcus sp. (OQ225631), a recently erected lineage within the redefined Stichococcus clade. Over a nine-day experimental incubation, 57.6% of diesel (~3.47 g/L) was removed via biosorption and biodegradation, demonstrating the strain’s potential for phytoremediation. Fourier transform infrared spectroscopy confirmed the adsorption of oil in accordance with its hydrophobic characteristics. Overall, degradation predominated over sorption of diesel. Chromatographic analysis confirmed that the strain efficiently metabolised medium-chain length n-alkanes (C-7 to C-21), particularly n-heneicosane. Mixotrophic cultivation using diesel as the organic carbon source under a constant light regime altered the car/chl-a ratio and triggered vacuolar activities. A small number of intracellular lipid droplets were observed on the seventh day of cultivation in transmission electron microscopic imaging. This is the first confirmation of diesel remediation ability in an Antarctic green microalga. Full article
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16 pages, 5375 KiB  
Article
Study of Archaeal Diversity in the Arctic Meltwater Lake Region
Biology 2023, 12(7), 1023; https://doi.org/10.3390/biology12071023 - 20 Jul 2023
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Abstract
Two typical lakes formed from meltwater in the Ny-Ålesund area were taken as the study subjects in 2018. To investigate the archaeal community compositions of the two lakes, 16S rRNA genes from soil samples from the intertidal and subtidal zones of the two [...] Read more.
Two typical lakes formed from meltwater in the Ny-Ålesund area were taken as the study subjects in 2018. To investigate the archaeal community compositions of the two lakes, 16S rRNA genes from soil samples from the intertidal and subtidal zones of the two lakes were sequenced with high throughput. At the phylum level, the intertidal zone was dominated by Crenarchaeota and the subtidal zone was dominated by Halobacter; at the genus level, the intertidal zone was dominated by Nitrososphaeraceae_unclassified and Candidatus_Nitrocosmicus, while the subtidal zone was dominated by Methanoregula. The soil physicochemical factors pH, moisture content (MC), total organic carbon (TOC), total organic nitrogen (TON), nitrite nitrogen (NO2-N), and nitrate nitrogen (NO3-N) were significantly different in the intertidal and subtidal zones of the lake. By redundancy analysis, the results indicated that NH4+-N, SiO32−-Si, MC, NO3-N, and NO2-N have had highly significant effects on the archaeal diversity and distribution. A weighted gene co-expression network analysis (WGCNA) was used to search for hub archaea associated with physicochemical factors. The results suggested that these physicochemical factors play important roles in the diversity and structure of the archaeal community at different sites by altering the abundance of certain hub archaea. In addition, Woesearchaeales was found to be the hub archaea genus at every site. Full article
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