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Kiss A, Hariri Akbari F, Marchev A, Papp V, Mirmazloum I. The Cytotoxic Properties of Extreme Fungi's Bioactive Components-An Updated Metabolic and Omics Overview. Life (Basel) 2023; 13:1623. [PMID: 37629481 PMCID: PMC10455657 DOI: 10.3390/life13081623] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 08/27/2023] Open
Abstract
Fungi are the most diverse living organisms on planet Earth, where their ubiquitous presence in various ecosystems offers vast potential for the research and discovery of new, naturally occurring medicinal products. Concerning human health, cancer remains one of the leading causes of mortality. While extensive research is being conducted on treatments and their efficacy in various stages of cancer, finding cytotoxic drugs that target tumor cells with no/less toxicity toward normal tissue is a significant challenge. In addition, traditional cancer treatments continue to suffer from chemical resistance. Fortunately, the cytotoxic properties of several natural products derived from various microorganisms, including fungi, are now well-established. The current review aims to extract and consolidate the findings of various scientific studies that identified fungi-derived bioactive metabolites with antitumor (anticancer) properties. The antitumor secondary metabolites identified from extremophilic and extremotolerant fungi are grouped according to their biological activity and type. It became evident that the significance of these compounds, with their medicinal properties and their potential application in cancer treatment, is tremendous. Furthermore, the utilization of omics tools, analysis, and genome mining technology to identify the novel metabolites for targeted treatments is discussed. Through this review, we tried to accentuate the invaluable importance of fungi grown in extreme environments and the necessity of innovative research in discovering naturally occurring bioactive compounds for the development of novel cancer treatments.
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Affiliation(s)
- Attila Kiss
- Agro-Food Science Techtransfer and Innovation Centre, Faculty for Agro, Food and Environmental Science, Debrecen University, 4032 Debrecen, Hungary;
| | - Farhad Hariri Akbari
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Andrey Marchev
- Laboratory of Metabolomics, Department of Biotechnology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 4000 Plovdiv, Bulgaria
| | - Viktor Papp
- Department of Botany, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Hungary;
| | - Iman Mirmazloum
- Department of Plant Physiology and Plant Ecology, Institute of Agronomy, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Hungary
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Liu Z, Liu G, Guo X, Li Y, Ji N, Xu X, Sun Q, Yang J. Diversity of the protease-producing bacteria and their extracellular protease in the coastal mudflat of Jiaozhou Bay, China: in response to clam naturally growing and aquaculture. Front Microbiol 2023; 14:1164937. [PMID: 37275176 PMCID: PMC10236810 DOI: 10.3389/fmicb.2023.1164937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/24/2023] [Indexed: 06/07/2023] Open
Abstract
The booming mudflat aquaculture poses an accumulation of organic matter and a certain environmental threat. Protease-producing bacteria are key players in regulating the nitrogen content in ecosystems. However, knowledge of the diversity of protease-producing bacteria in coastal mudflats is limited. This study investigated the bacterial diversity in the coastal mudflat, especially protease-producing bacteria and their extracellular proteases, by using culture-independent methods and culture-dependent methods. The clam aquaculture area exhibited a higher concentration of carbon, nitrogen, and phosphorus when compared with the non-clam area, and a lower richness and diversity of bacterial community when compared with the clam naturally growing area. The major classes in the coastal mud samples were Bacteroidia, Gammaproteobacteria, and Alphaproteobacteria. The Bacillus-like bacterial community was the dominant cultivated protease-producing group, accounting for 52.94% in the non-clam area, 30.77% in the clam naturally growing area, and 50% in the clam aquaculture area, respectively. Additionally, serine protease and metalloprotease were the principal extracellular protease of the isolated coastal bacteria. These findings shed light on the understanding of the microbes involved in organic nitrogen degradation in coastal mudflats and lays a foundation for the development of novel protease-producing bacterial agents for coastal mudflat purification.
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Affiliation(s)
- Zhiyun Liu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Guangchao Liu
- College of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Xuzhen Guo
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Yang Li
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
- Qingdao Special Food Research Institute, Qingdao, China
| | - Na Ji
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
- Qingdao Special Food Research Institute, Qingdao, China
| | - Xingfeng Xu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
- Qingdao Special Food Research Institute, Qingdao, China
| | - Qingjie Sun
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
- Qingdao Special Food Research Institute, Qingdao, China
| | - Jie Yang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
- Qingdao Special Food Research Institute, Qingdao, China
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Shaffer JMC, Giddings LA, Samples RM, Mikucki JA. Genomic and phenotypic characterization of a red-pigmented strain of Massilia frigida isolated from an Antarctic microbial mat. Front Microbiol 2023; 14:1156033. [PMID: 37250028 PMCID: PMC10213415 DOI: 10.3389/fmicb.2023.1156033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/20/2023] [Indexed: 05/31/2023] Open
Abstract
The McMurdo Dry Valleys of Antarctica experience a range of selective pressures, including extreme seasonal variation in temperature, water and nutrient availability, and UV radiation. Microbial mats in this ecosystem harbor dense concentrations of biomass in an otherwise desolate environment. Microbial inhabitants must mitigate these selective pressures via specialized enzymes, changes to the cellular envelope, and the production of secondary metabolites, such as pigments and osmoprotectants. Here, we describe the isolation and characterization of a Gram-negative, rod-shaped, motile, red-pigmented bacterium, strain DJPM01, from a microbial mat within the Don Juan Pond Basin of Wright Valley. Analysis of strain DJMP01's genome indicates it can be classified as a member of the Massilia frigida species. The genome contains several genes associated with cold and salt tolerance, including multiple RNA helicases, protein chaperones, and cation/proton antiporters. In addition, we identified 17 putative secondary metabolite gene clusters, including a number of nonribosomal peptides and ribosomally synthesized and post-translationally modified peptides (RiPPs), among others, and the biosynthesis pathway for the antimicrobial pigment prodigiosin. When cultivated on complex agar, multiple prodiginines, including the antibiotic prodigiosin, 2-methyl-3-propyl-prodiginine, 2-methyl-3-butyl-prodiginine, 2-methyl-3-heptyl-prodiginine, and cycloprodigiosin, were detected by LC-MS. Genome analyses of sequenced members of the Massilia genus indicates prodigiosin production is unique to Antarctic strains. UV-A radiation, an ecological stressor in the Antarctic, was found to significantly decrease the abundance of prodiginines produced by strain DJPM01. Genomic and phenotypic evidence indicates strain DJPM01 can respond to the ecological conditions of the DJP microbial mat, with prodiginines produced under a range of conditions, including extreme UV radiation.
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Affiliation(s)
- Jacob M. C. Shaffer
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
| | | | - Robert M. Samples
- Department of Chemistry, Smith College, Northampton, MA, United States
| | - Jill A. Mikucki
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
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Tveit AT, Söllinger A, Rainer EM, Didriksen A, Hestnes AG, Motleleng L, Hellinger HJ, Rattei T, Svenning MM. Thermal acclimation of methanotrophs from the genus Methylobacter. THE ISME JOURNAL 2023; 17:502-513. [PMID: 36650275 PMCID: PMC10030640 DOI: 10.1038/s41396-023-01363-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/30/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023]
Abstract
Methanotrophs oxidize most of the methane (CH4) produced in natural and anthropogenic ecosystems. Often living close to soil surfaces, these microorganisms must frequently adjust to temperature change. While many environmental studies have addressed temperature effects on CH4 oxidation and methanotrophic communities, there is little knowledge about the physiological adjustments that underlie these effects. We have studied thermal acclimation in Methylobacter, a widespread, abundant, and environmentally important methanotrophic genus. Comparisons of growth and CH4 oxidation kinetics at different temperatures in three members of the genus demonstrate that temperature has a strong influence on how much CH4 is consumed to support growth at different CH4 concentrations. However, the temperature effect varies considerably between species, suggesting that how a methanotrophic community is composed influences the temperature effect on CH4 uptake. To understand thermal acclimation mechanisms widely we carried out a transcriptomics experiment with Methylobacter tundripaludum SV96T. We observed, at different temperatures, how varying abundances of transcripts for glycogen and protein biosynthesis relate to cellular glycogen and ribosome concentrations. Our data also demonstrated transcriptional adjustment of CH4 oxidation, oxidative phosphorylation, membrane fatty acid saturation, cell wall composition, and exopolysaccharides between temperatures. In addition, we observed differences in M. tundripaludum SV96T cell sizes at different temperatures. We conclude that thermal acclimation in Methylobacter results from transcriptional adjustment of central metabolism, protein biosynthesis, cell walls and storage. Acclimation leads to large shifts in CH4 consumption and growth efficiency, but with major differences between species. Thus, our study demonstrates that physiological adjustments to temperature change can substantially influence environmental CH4 uptake rates and that consideration of methanotroph physiology might be vital for accurate predictions of warming effects on CH4 emissions.
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Affiliation(s)
- Alexander T Tveit
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway.
| | - Andrea Söllinger
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Edda Marie Rainer
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Alena Didriksen
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Anne Grethe Hestnes
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Liabo Motleleng
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Hans-Jörg Hellinger
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
- University of Vienna, Doctoral School in Microbiology and Environmental Science, Vienna, Austria
| | - Thomas Rattei
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
| | - Mette M Svenning
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
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Verma A, Amnebrink D, Pinhassi J, Wikner J. Prokaryotic maintenance respiration and growth efficiency field patterns reproduced by temperature and nutrient control at mesocosm scale. Environ Microbiol 2023; 25:721-737. [PMID: 36511634 DOI: 10.1111/1462-2920.16300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
The distribution of prokaryotic metabolism between maintenance and growth activities has a profound impact on the transformation of carbon substrates to either biomass or CO2 . Knowledge of key factors influencing prokaryotic maintenance respiration is, however, highly limited. This mesocosm study validated the significance of prokaryotic maintenance respiration by mimicking temperature and nutrients within levels representative of winter and summer conditions. A global range of growth efficiencies (0.05-0.57) and specific growth rates (0.06-2.7 d-1 ) were obtained. The field pattern of cell-specific respiration versus specific growth rate and the global relationship between growth efficiency and growth rate were reproduced. Maintenance respiration accounted for 75% and 15% of prokaryotic respiration corresponding to winter and summer conditions, respectively. Temperature and nutrients showed independent positive effects for all prokaryotic variables except abundance and cell-specific respiration. All treatments resulted in different taxonomic diversity, with specific populations of amplicon sequence variants associated with either maintenance or growth conditions. These results validate a significant relationship between specific growth and respiration rate under productive conditions and show that elevated prokaryotic maintenance respiration can occur under cold and oligotrophic conditions. The experimental design provides a tool for further study of prokaryotic energy metabolism under realistic conditions at the mesocosm scale.
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Affiliation(s)
- Ashish Verma
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Umeå Marine Sciences Centre, Hörnefors, Sweden
| | - Dennis Amnebrink
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Johan Wikner
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Umeå Marine Sciences Centre, Hörnefors, Sweden
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Liao X, Shen W, Wang Y, Bai L, Ding T. Microbial contamination, community diversity and cross-contamination risk of food-contact ice. Food Res Int 2023; 164:112335. [PMID: 36737928 DOI: 10.1016/j.foodres.2022.112335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 11/05/2022] [Accepted: 12/18/2022] [Indexed: 12/29/2022]
Abstract
Ice is widely used in the food industry, as an ingredient (edible ice) directly added to food or as a coolant (food-contact ice) for fresh food preservation along the cold chain. However, it has been shown that food-contact ice are easily polluted by pathogens, potentially endangering the public's health. In the present study, the hygiene status of food-contact ice collected from various sources (local farmer markets, supermarkets, and restaurants) was evaluated through the quantitative estimation of total bacterial counts and coliform counts as well as the prevalence of foodborne pathogenic bacteria (Staphylococcus aureus, Vibrio parahaemolyticus, Salmonella, Listeria monocytogenes, Shigella). The average levels of total bacterial counts in the ice for preserving the aquatic products, poultry meat and livestock meat are 4.88, 4.18 and 6.11 log10 CFU/g, respectively. Over 90 % of the food-contact ice were positive for coliforms. The detection rate of S. aureus in all the food-contact ice samples was highest, followed by Salmonella, V. parahaemolyticus and L. monocytogenes, and Shigella was not detected. In addition, the bacterial community diversity of food-contact ice was analyzed with high-throughput sequencing. The dominant bacteria taxa in food-contact ice are heavily dependent on the environment of sampling sites. The predicted phenotypes of biofilm forming, oxidative stress tolerance, mobile element containing and pathogenesis were identified in the bacteria taxa of food-contact ice, which should be carefully evaluated in future work. Finally, the cross-contamination models of pathogen transfer during ice preservation were established. The results showed that the transfer rates of ice-isolated S. aureus between food and ice were significantly higher than that of V. parahaemolyticus. The binomial distribution B(n, p) exhibited a better fitness to describe the pathogen transfer during ice preservation when the transfer rate was low, in turn, the transfer rate-based probability model showed a better fit to the data when the transfer rate was high. Monte Carlo simulation with Latin-Hypercube sampling was carried out to predict the contamination levels of S. aureus and V. parahaemolyticus on food as the result of cross contamination during ice preservation ranging from -2.90 to 2.96 log10 CFU/g with a 90 % confidence interval. The findings of this work are conducive to a comprehensive understanding of the current hygiene status of food-contact ice, and lay a theoretical foundation for the risk assessment of cross-contamination during ice preservation.
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Affiliation(s)
- Xinyu Liao
- School of Mechanical and Energy Engineering, Ningbotech University, Ningbo, China; Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang 310058, China; Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, 314100 Jiaxing, China
| | - Wangwang Shen
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yeru Wang
- Key Laboratory of Food Safety Risk Assessment, National Health Commission of the People's Republic of China, China National Center for Food Safety Risk Assessment, Beijing 100022, China
| | - Li Bai
- Key Laboratory of Food Safety Risk Assessment, National Health Commission of the People's Republic of China, China National Center for Food Safety Risk Assessment, Beijing 100022, China
| | - Tian Ding
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang 310058, China; Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, 314100 Jiaxing, China.
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Reconstruction and Analysis of Thermodynamically Constrained Models Reveal Metabolic Responses of a Deep-Sea Bacterium to Temperature Perturbations. mSystems 2022; 7:e0058822. [PMID: 35950761 PMCID: PMC9426432 DOI: 10.1128/msystems.00588-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Microbial acclimation to different temperature conditions can involve broad changes in cell composition and metabolic efficiency. A systems-level view of these metabolic responses in nonmesophilic organisms, however, is currently missing. In this study, thermodynamically constrained genome-scale models were applied to simulate the metabolic responses of a deep-sea psychrophilic bacterium, Shewanella psychrophila WP2, under suboptimal (4°C), optimal (15°C), and supraoptimal (20°C) growth temperatures. The models were calibrated with experimentally determined growth rates of WP2. Gibbs free energy change of reactions (ΔrG'), metabolic fluxes, and metabolite concentrations were predicted using random simulations to characterize temperature-dependent changes in the metabolism. The modeling revealed the highest metabolic efficiency at the optimal temperature, and it suggested distinct patterns of ATP production and consumption that could lead to lower metabolic efficiency under suboptimal or supraoptimal temperatures. The modeling also predicted rearrangement of fluxes through multiple metabolic pathways, including the glycolysis pathway, Entner-Doudoroff pathway, tricarboxylic acid (TCA) cycle, and electron transport system, and these predictions were corroborated through comparisons to WP2 transcriptomes. Furthermore, predictions of metabolite concentrations revealed the potential conservation of reducing equivalents and ATP in the suboptimal temperature, consistent with experimental observations from other psychrophiles. Taken together, the WP2 models provided mechanistic insights into the metabolism of a psychrophile in response to different temperatures. IMPORTANCE Metabolic flexibility is a central component of any organism's ability to survive and adapt to changes in environmental conditions. This study represents the first application of thermodynamically constrained genome-scale models in simulating the metabolic responses of a deep-sea psychrophilic bacterium to various temperatures. The models predicted differences in metabolic efficiency that were attributed to changes in metabolic pathway utilization and metabolite concentration during growth under optimal and nonoptimal temperatures. Experimental growth measurements were used for model calibration, and temperature-dependent transcriptomic changes corroborated the model-predicted rearrangement of metabolic fluxes. Overall, this study highlights the utility of modeling approaches in studying the temperature-driven metabolic responses of an extremophilic organism.
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Acevedo-Barrios R, Rubiano-Labrador C, Navarro-Narvaez D, Escobar-Galarza J, González D, Mira S, Moreno D, Contreras A, Miranda-Castro W. Perchlorate-reducing bacteria from Antarctic marine sediments. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 194:654. [PMID: 35934758 DOI: 10.1007/s10661-022-10328-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Perchlorate is a contaminant that can persist in groundwater and soil, and is frequently detected in different ecosystems at concentrations relevant to human health. This study isolated and characterised halotolerant bacteria that can potentially perform perchlorate reduction. Bacterial microorganisms were isolated from marine sediments on Deception, Horseshoe and Half Moon Islands of Antarctica. The results of the 16S ribosomal RNA (rRNA) gene sequence analysis indicated that the isolates were phylogenetically related to Psychrobacter cryohalolentis, Psychrobacter urativorans, Idiomarina loihiensis, Psychrobacter nivimaris, Sporosarcina aquimarina and Pseudomonas lactis. The isolates grew at a sodium chloride concentration of up to 30% and a perchlorate concentration of up to 10,000 mg/L, which showed their ability to survive in saline conditions and high perchlorate concentrations. Between 21.6 and 40% of perchlorate was degraded by the isolated bacteria. P. cryohalolentis and P. urativorans degraded 30.3% and 32.6% of perchlorate, respectively. I. loihiensis degraded 40% of perchlorate, and P. nivimaris, S. aquimarina and P. lactis degraded 22%, 21.8% and 21.6% of perchlorate, respectively. I. loihiensis had the highest reduction in perchlorate, whereas P. lactis had the lowest reduction. This study is significant as it is the first finding of P. cryohalolentis and. P. lactis on the Antarctic continent. In conclusion, these bacteria isolated from marine sediments on Antarctica offer promising resources for the bioremediation of perchlorate contamination due to their ability to degrade perchlorate, showing their potential use as a biological system to reduce perchlorate in high-salinity ecosystems.
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Affiliation(s)
- Rosa Acevedo-Barrios
- Grupo de Estudios Químicos Y Biológicos, Universidad Tecnológica de Bolívar, 130010, Cartagena, Colombia.
| | - Carolina Rubiano-Labrador
- Grupo de Estudios Químicos Y Biológicos, Universidad Tecnológica de Bolívar, 130010, Cartagena, Colombia
| | - Dhania Navarro-Narvaez
- Grupo de Estudios Químicos Y Biológicos, Universidad Tecnológica de Bolívar, 130010, Cartagena, Colombia
| | - Johana Escobar-Galarza
- Grupo de Estudios Químicos Y Biológicos, Universidad Tecnológica de Bolívar, 130010, Cartagena, Colombia
| | - Diana González
- Grupo de Estudios Químicos Y Biológicos, Universidad Tecnológica de Bolívar, 130010, Cartagena, Colombia
| | - Stephanie Mira
- Grupo de Estudios Químicos Y Biológicos, Universidad Tecnológica de Bolívar, 130010, Cartagena, Colombia
| | - Dayana Moreno
- Grupo de Estudios Químicos Y Biológicos, Universidad Tecnológica de Bolívar, 130010, Cartagena, Colombia
| | - Aura Contreras
- Grupo de Estudios Químicos Y Biológicos, Universidad Tecnológica de Bolívar, 130010, Cartagena, Colombia
| | - Wendy Miranda-Castro
- Grupo de Estudios Químicos Y Biológicos, Universidad Tecnológica de Bolívar, 130010, Cartagena, Colombia
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Transcriptomic Profiling Revealed Signaling Pathways Associated with the Spawning of Female Zebrafish under Cold Stress. Int J Mol Sci 2022; 23:ijms23147494. [PMID: 35886843 PMCID: PMC9320639 DOI: 10.3390/ijms23147494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 12/13/2022] Open
Abstract
As one of the critical abiotic factors, temperature controls fish development and reproduction. However, the effects of low temperature on the transcriptional regulation of zebrafish reproduction remain largely unclear. In this study, the fecundity of zebrafish was examined after exposure to cold temperatures at 19.5 °C, 19 °C, 18.5 °C, or 18 °C. The temperature at 19 °C showed no significant influence on the fecundity of zebrafish, but temperature at 18.5 °C or 18 °C significantly blocked the spawning of females, suggesting the existence of a low temperature critical point for the spawning of zebrafish females. Based on these observations, the brains of anesthetized fish under cold stress at different cold temperatures were collected for high-throughput RNA-seq assays. Key genes, hub pathways and important biological processes responding to cold temperatures during the spawning of zebrafish were identified through bioinformatic analysis. The number of down-regulated and up-regulated genes during the temperature reduction from egg-spawning temperatures at 19.5 °C and 19 °C to non-spawning temperatures at 18.5 °C and 18 °C were 2588 and 2527 (fold change ≥ 1.5 and p-value ≤ 0.01), respectively. Venn analysis was performed to identify up- and down-regulated key genes. KEGG enrichment analysis indicated that the hub pathways overrepresented among down-regulated key genes included the GnRH signaling pathway, vascular smooth muscle contraction, C-type lectin receptor signaling pathway, phosphatidylinositol signaling system and insulin signaling pathway. GO enrichment analysis of down-regulated key genes revealed the most important biological processes inhibited under non-spawning temperatures at 18.5 °C and 18 °C were photoreceptor cell outer segment organization, circadian regulation of gene expression and photoreceptor cell maintenance. Furthermore, 99 hormone-related genes were found in the brain tissues of non-spawning and spawning groups, and GnRH signaling pathway and insulin signaling pathway were enriched from down-regulated genes related to hormones at 18.5 °C and 18 °C. Thus, these findings uncovered crucial hormone-related genes and signaling pathways controlling the spawning of female zebrafish under cold stress.
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Vishnivetskaya TA, Mironov VA, Abramov AA, Shcherbakova VA, Rivkina EM. Biogeochemical Characteristics of Earth's Volcanic Permafrost: An Analog of Extraterrestrial Environments. ASTROBIOLOGY 2022; 22:812-828. [PMID: 35333595 DOI: 10.1089/ast.2021.0137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This article describes a study of frozen volcanic deposits collected from volcanoes Tolbachik and Bezymianny on the Kamchatka Peninsula, Russia, and Deception Island volcano, Antarctica. In addition, we studied suprasnow ash layers deposited after the 2007 eruptions of volcanoes Shiveluch and Bezymianny on Kamchatka. The main objectives were to characterize the presence and survivability of thermophilic microorganisms in perennially frozen volcanic deposits. As opposed to permafrost from the polar regions, viable thermophiles were detected in volcanic permafrost by cultivation, microscopy, and sequencing. In the permafrost of Tolbachik volcano, we observed methane formation by both psychrophilic and thermophilic methanogenic archaea, while at 37°C, methane production was noticeably lower. Thermophilic bacteria isolated from volcanic permafrost from the Deception Island were 99.93% related to Geobacillus stearothermophilus. Our data showed biological sulfur reduction to sulfide at 85°C and even at 130°C, where hyperthermophilic archaea of the genus Thermoproteus were registered. Sequences of hyperthermophilic bacteria of the genus Caldicellulosiruptor were discovered in clone libraries from fresh volcanic ash deposited on snow. Microorganisms found in volcanic terrestrial permafrost may serve as a model for the alien inhabitants of Mars, a cryogenic planet with numerous volcanoes. Thermophiles and hyperthermophiles and their metabolic processes represent a guideline for the future exploration missions on Mars.
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Affiliation(s)
- Tatiana A Vishnivetskaya
- Institute of Physicochemical and Biological Problems in Soil Science, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences," Pushchino, Russia
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
| | - Vasiliy A Mironov
- Institute of Physicochemical and Biological Problems in Soil Science, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences," Pushchino, Russia
| | - Andrey A Abramov
- Institute of Physicochemical and Biological Problems in Soil Science, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences," Pushchino, Russia
| | - Viktoria A Shcherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences," Pushchino, Russia
| | - Elizaveta M Rivkina
- Institute of Physicochemical and Biological Problems in Soil Science, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences," Pushchino, Russia
- Institute of Geography, Russian Academy of Sciences, Moscow, 119017, Russia
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11
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Ijaq J, Chandra D, Ray MK, Jagannadham MV. Investigating the Functional Role of Hypothetical Proteins From an Antarctic Bacterium Pseudomonas sp. Lz4W: Emphasis on Identifying Proteins Involved in Cold Adaptation. Front Genet 2022; 13:825269. [PMID: 35360867 PMCID: PMC8963723 DOI: 10.3389/fgene.2022.825269] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/07/2022] [Indexed: 11/28/2022] Open
Abstract
Exploring the molecular mechanisms behind bacterial adaptation to extreme temperatures has potential biotechnological applications. In the present study, Pseudomonas sp. Lz4W, a Gram-negative psychrophilic bacterium adapted to survive in Antarctica, was selected to decipher the molecular mechanism underlying the cold adaptation. Proteome analysis of the isolates grown at 4°C was performed to identify the proteins and pathways that are responsible for the adaptation. However, many proteins from the expressed proteome were found to be hypothetical proteins (HPs), whose function is unknown. Investigating the functional roles of these proteins may provide additional information in the biological understanding of the bacterial cold adaptation. Thus, our study aimed to assign functions to these HPs and understand their role at the molecular level. We used a structured insilico workflow combining different bioinformatics tools and databases for functional annotation. Pseudomonas sp. Lz4W genome (CP017432, version 1) contains 4493 genes and 4412 coding sequences (CDS), of which 743 CDS were annotated as HPs. Of these, from the proteome analysis, 61 HPs were found to be expressed consistently at the protein level. The amino acid sequences of these 61 HPs were submitted to our workflow and we could successfully assign a function to 18 HPs. Most of these proteins were predicted to be involved in biological mechanisms of cold adaptations such as peptidoglycan metabolism, cell wall organization, ATP hydrolysis, outer membrane fluidity, catalysis, and others. This study provided a better understanding of the functional significance of HPs in cold adaptation of Pseudomonas sp. Lz4W. Our approach emphasizes the importance of addressing the “hypothetical protein problem” for a thorough understanding of mechanisms at the cellular level, as well as, provided the assessment of integrating proteomics methods with various annotation and curation approaches to characterize hypothetical or uncharacterized protein data. The MS proteomics data generated from this study has been deposited to the ProteomeXchange through PRIDE with the dataset identifier–PXD029741.
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Affiliation(s)
- Johny Ijaq
- Metabolomics Facility, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Deepika Chandra
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Malay Kumar Ray
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - M. V. Jagannadham
- Metabolomics Facility, School of Life Sciences, University of Hyderabad, Hyderabad, India
- *Correspondence: M. V. Jagannadham,
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12
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Šantl-Temkiv T, Amato P, Casamayor EO, Lee PKH, Pointing SB. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6524182. [PMID: 35137064 PMCID: PMC9249623 DOI: 10.1093/femsre/fuac009] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/31/2022] [Accepted: 02/06/2022] [Indexed: 11/30/2022] Open
Abstract
The atmosphere connects habitats across multiple spatial scales via airborne dispersal of microbial cells, propagules and biomolecules. Atmospheric microorganisms have been implicated in a variety of biochemical and biophysical transformations. Here, we review ecological aspects of airborne microorganisms with respect to their dispersal, activity and contribution to climatic processes. Latest studies utilizing metagenomic approaches demonstrate that airborne microbial communities exhibit pronounced biogeography, driven by a combination of biotic and abiotic factors. We quantify distributions and fluxes of microbial cells between surface habitats and the atmosphere and place special emphasis on long-range pathogen dispersal. Recent advances have established that these processes may be relevant for macroecological outcomes in terrestrial and marine habitats. We evaluate the potential biological transformation of atmospheric volatile organic compounds and other substrates by airborne microorganisms and discuss clouds as hotspots of microbial metabolic activity in the atmosphere. Furthermore, we emphasize the role of microorganisms as ice nucleating particles and their relevance for the water cycle via formation of clouds and precipitation. Finally, potential impacts of anthropogenic forcing on the natural atmospheric microbiota via emission of particulate matter, greenhouse gases and microorganisms are discussed.
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Affiliation(s)
- Tina Šantl-Temkiv
- Department of Biology, Aarhus University, DK-8000 Aarhus, Denmark
- Stellar Astrophysics Centre, Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus, Denmark
| | - Pierre Amato
- Institut de Chimie de Clermont-Ferrand, SIGMA Clermont, CNRS, Université Clermont Auvergne, 63178, Clermont-Ferrand, France
| | - Emilio O Casamayor
- Centre for Advanced Studies of Blanes, Spanish Council for Research (CSIC), 17300, Blanes, Spain
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China
| | - Stephen B Pointing
- Corresponding author: Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore 138527. Tel: +65 6601 1000; E-mail:
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13
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Duan J, Guo W. The cold adaption profiles of Pseudoalteromonas shioyasakiensis D1497 from Yap trench to cope with cold. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 32:e00689. [PMID: 34987981 PMCID: PMC8711050 DOI: 10.1016/j.btre.2021.e00689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/01/2021] [Accepted: 11/11/2021] [Indexed: 01/08/2023]
Abstract
P. shioyasakiensis D1497converted more substrate into biomass at low temperature. P. shioyasakiensis D1497 prefered to use codons with A/T in the third position. The energy metabolism related genes were down regulated in cold environment. P. shioyasakiensis D1497 presented an energy saving metabolism strategy to cope with cold.
Genome sequencing of Pseudoalteromonas shioyasakiensis D1497, a psychrophile from the Yap trench, revealed that it contained a circle chromosome of 3,631,285 bp with 40.94% GC content and prefered to use codons with A/T in the third position. Additionally, the relative synonymous codon usage (RSCU) values indicated the codons with A and T in the third position were always the most used. Cultivation of P. shioyasakiensis D1497 presented lower substrate consumption rate, higher ATP pool and higher conversion rate of biomass per unit substrate consumed at low temperature (15 °C) than that of the room temperature (25 °C) culture. Comparative transcriptomic analysis revealed that the mRNA abundance of energy metabolism related genes was decreased in 15 °C culture compared with that of 25 °C culture. In addition to its codon usage biases profile, P. shioyasakiensis D1497 presented an energy saving metabolism strategy to cope with cold, converting more carbon source into biomass in cold environment.
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Affiliation(s)
- Jingjing Duan
- College of Environment and Ecology, Xiamen University, Xiamen 361005, Fujian, China
| | - Wenbin Guo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, Fujian, China
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14
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Péguilhan R, Besaury L, Rossi F, Enault F, Baray JL, Deguillaume L, Amato P. Rainfalls sprinkle cloud bacterial diversity while scavenging biomass. FEMS Microbiol Ecol 2021; 97:6420242. [PMID: 34734249 DOI: 10.1093/femsec/fiab144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/27/2021] [Indexed: 11/15/2022] Open
Abstract
Bacteria circulate in the atmosphere, through clouds and precipitation to surface ecosystems. Here, we conducted a coordinated study of bacteria assemblages in clouds and precipitation at two sites distant of ∼800 m in elevation in a rural vegetated area around puy de Dôme Mountain, France, and analysed them in regard to meteorological, chemical and air masses' history data. In both clouds and precipitation, bacteria generally associated with vegetation or soil dominated. Elevated ATP-to-cell ratio in clouds compared with precipitation suggested a higher proportion of viable cells and/or specific biological processes. The increase of bacterial cell concentration from clouds to precipitation indicated strong below-cloud scavenging. Using ions as tracers, we derive that 0.2 to 25.5% of the 1.1 × 107 to 6.6 × 108 bacteria cell/m2/h1 deposited with precipitation originated from the source clouds. Yet, the relative species richness decreased with the proportion of inputs from clouds, pointing them as sources of distant microbial diversity. Biodiversity profiles, thus, differed between clouds and precipitation in relation with distant/local influencing sources, and potentially with bacterial phenotypic traits. Notably Undibacterium, Bacillus and Staphylococcus were more represented in clouds, while epiphytic bacteria such as Massilia, Sphingomonas, Rhodococcus and Pseudomonas were enriched in precipitation.
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Affiliation(s)
- Raphaëlle Péguilhan
- Université Clermont Auvergne, CNRS, SIGMA Clermont , ICCF, F-63000 CLERMONT-FERRAND, France
| | - Ludovic Besaury
- Université Clermont Auvergne, CNRS, SIGMA Clermont , ICCF, F-63000 CLERMONT-FERRAND, France
| | - Florent Rossi
- Université Clermont Auvergne, CNRS, SIGMA Clermont , ICCF, F-63000 CLERMONT-FERRAND, France
| | - François Enault
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome et Environnement, F-63000 CLERMONT-FERRAND, France
| | - Jean-Luc Baray
- Université Clermont Auvergne, CNRS, Observatoire de Physique du Globe de Clermont-Ferrand , UMS 833, F-63000 CLERMONT-FERRAND, France.,Université Clermont Auvergne, CNRS, Laboratoire de Météorologie Physique , UMR 6016, F-63000 CLERMONT-FERRAND, France
| | - Laurent Deguillaume
- Université Clermont Auvergne, CNRS, Observatoire de Physique du Globe de Clermont-Ferrand , UMS 833, F-63000 CLERMONT-FERRAND, France.,Université Clermont Auvergne, CNRS, Laboratoire de Météorologie Physique , UMR 6016, F-63000 CLERMONT-FERRAND, France
| | - Pierre Amato
- Université Clermont Auvergne, CNRS, SIGMA Clermont , ICCF, F-63000 CLERMONT-FERRAND, France
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15
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Ijoma GN, Nkuna R, Mutungwazi A, Rashama C, Matambo TS. Applying PICRUSt and 16S rRNA functional characterisation to predicting co-digestion strategies of various animal manures for biogas production. Sci Rep 2021; 11:19913. [PMID: 34620937 PMCID: PMC8497515 DOI: 10.1038/s41598-021-99389-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/24/2021] [Indexed: 02/08/2023] Open
Abstract
An estimated 25 million tons of animal manure is produced globally every year, causing considerable impact to the environment. These impacts can be managed through the use of anaerobic digestion (AD) This process achieves waste degradation through enzymatic activity, the efficiency of the AD process is directly related to microorganisms that produce these enzymes. Biomethane potential (BMP) assays remain the standard theoretical framework to pre-determine biogas yield and have been used to determine the feasibility of substrates or their combination for biogas production. However, an integrated approach that combines substrate choice and co-digestion would provide an improvement to the current predictive models. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) addresses the limitations of assays in this regard. In this paper, the biochemical functions of horse, cow, and pig manures are predicted. A total of 135 predicted KEGG Orthologies (KOs) showed amino acids, carbohydrate, energy, lipid, and xenobiotic metabolisms in all the samples. Linear discriminant analysis (LDA) combined with the effect size measurements (LEfSe), showed that fructose, mannose, amino acid and nucleotide sugar, phosphotransferase (PST) as well as starch and sucrose metabolisms were significantly higher in horse manure samples. 36 of the KOs were related to the acidogenesis and/or acetogenesis AD stages. Extended bar plots showed that 11 significant predictions were observed for horse-cow, while 5 were predicted for horse-pig and for cow-pig manures. Based on these predictions, the AD process can be enhanced through co-digestion strategies that takes into account the predicted metabolic contributions of the manure samples. The results supported the BMP calculations for the samples in this study. Biogas yields can be improved if this combined approach is employed in routine analysis before co-digesting different substrates.
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Affiliation(s)
- Grace N Ijoma
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort, 1709, South Africa.
| | - Rosina Nkuna
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort, 1709, South Africa
| | - Asheal Mutungwazi
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort, 1709, South Africa
| | - Charles Rashama
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort, 1709, South Africa
| | - Tonderayi S Matambo
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort, 1709, South Africa
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16
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Adaptive remodelling of blue pigmenting Pseudomonas fluorescens pf59 proteome in response to different environmental conditions. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Yang Y, Chen N, Sun L, Zhang Y, Wu Y, Wang Y, Liao X, Mi J. Short-term cold stress can reduce the abundance of antibiotic resistance genes in the cecum and feces in a pig model. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125868. [PMID: 34492815 DOI: 10.1016/j.jhazmat.2021.125868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 06/13/2023]
Abstract
Comprehensive studies on the effects of cold stress on antibiotic resistance genes (ARGs) in the intestines and feces remain scarce. In this study, pigs were selected as the animal model and divided into a normal temperature group and a 48-h short-term cold stress group. The ARG profiles in fecal, cecal content and cecal mucosa samples were analyzed. The results showed that the normalized abundance of ARGs in the cecal mucosa samples in the cold stress group was significantly higher than that in the normal temperature group, while the normalized ARG abundances in the fecal and cecal content samples were significantly lower than those in the normal temperature group (P < 0.05). The bacterial community composition (especially Firmicutes) was the major driver impacting the ARG profile and accounted for 32.2% of the variation in the ARG profile, followed by metabolites (especially creatinine and oxypurinol) and mobile genetic elements (MGEs) (especially plasmids and insertion elements). And it was found that creatinine and oxypurinol can reduce the abundance of ARGs and Firmicutes in the in vitro experiment. The results indicate that short-term cold stress can reduce the abundance of ARGs in the cecum and feces of pigs, providing reference data for environmental safety.
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Affiliation(s)
- Yiwen Yang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Ningxue Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Lan Sun
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Yu Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Yinbao Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Tropical Agricultural Environment, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Yan Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Tropical Agricultural Environment, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xindi Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Tropical Agricultural Environment, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Jiandui Mi
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Tropical Agricultural Environment, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
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18
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Genomics and transcriptomics analyses provide insights into the cold adaptation strategies of an Antarctic bacterium, Cryobacterium sp. SO1. Polar Biol 2021. [DOI: 10.1007/s00300-021-02883-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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19
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Abramov A, Vishnivetskaya T, Rivkina E. Are permafrost microorganisms as old as permafrost? FEMS Microbiol Ecol 2021; 97:6143815. [PMID: 33601419 DOI: 10.1093/femsec/fiaa260] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/23/2020] [Indexed: 11/13/2022] Open
Abstract
Permafrost describes the condition of earth material (sand, ground, organic matter, etc.) cemented by ice when its temperature remains at or below 0°C continuously for longer than 2 years. Evidently, permafrost is as old as the time passed from freezing of the earth material. Permafrost is a unique phenomenon and may preserve life forms it encloses. Therefore, in order to talk confidently about the preservation of paleo-objects in permafrost, knowledge about the geological age of sediments, i.e. when the sediments were formed, and permafrost age, when those sediments became permanently frozen, is essential. There are two types of permafrost-syngenetic and epigenetic. The age of syngenetic permafrost corresponds to the geological age of its sediments, whereas the age of epigenetic permafrost is less than the geological age of its sediments. Both of these formations preserve microorganisms and their metabolic products; however, the interpretations of the microbiological and molecular-biological data are inconsistent. This paper reviews the current knowledge of time-temperature history and age of permafrost in relation to available microbiological and metagenomic data.
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Affiliation(s)
- Andrey Abramov
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Tatiana Vishnivetskaya
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino 142290, Russia.,University of Tennessee, Center for Environmental Biotechnology, Knoxville, TN 37996, USA
| | - Elizaveta Rivkina
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino 142290, Russia
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20
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Taylor M, Lukowski JK, Anderton CR. Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:872-894. [PMID: 33656885 PMCID: PMC8033567 DOI: 10.1021/jasms.0c00439] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 05/02/2023]
Abstract
Biological systems are composed of heterogeneous populations of cells that intercommunicate to form a functional living tissue. Biological function varies greatly across populations of cells, as each single cell has a unique transcriptome, proteome, and metabolome that translates to functional differences within single species and across kingdoms. Over the past decade, substantial advancements in our ability to characterize omic profiles on a single cell level have occurred, including in multiple spectroscopic and mass spectrometry (MS)-based techniques. Of these technologies, spatially resolved mass spectrometry approaches, including mass spectrometry imaging (MSI), have shown the most progress for single cell proteomics and metabolomics. For example, reporter-based methods using heavy metal tags have allowed for targeted MS investigation of the proteome at the subcellular level, and development of technologies such as laser ablation electrospray ionization mass spectrometry (LAESI-MS) now mean that dynamic metabolomics can be performed in situ. In this Perspective, we showcase advancements in single cell spatial metabolomics and proteomics over the past decade and highlight important aspects related to high-throughput screening, data analysis, and more which are vital to the success of achieving proteomic and metabolomic profiling at the single cell scale. Finally, using this broad literature summary, we provide a perspective on how the next decade may unfold in the area of single cell MS-based proteomics and metabolomics.
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Affiliation(s)
- Michael
J. Taylor
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jessica K. Lukowski
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Christopher R. Anderton
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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21
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Sukumaran L, Radhakrishnan M. Effect of frozen storage on the inhibition of microbial population, chemical and sensory characteristics of coconut neera. J Appl Microbiol 2021; 131:1830-1839. [PMID: 33721389 DOI: 10.1111/jam.15068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/07/2021] [Accepted: 03/09/2021] [Indexed: 11/27/2022]
Abstract
AIM In this study, the effect of frozen storage on the inhibition of microbial population in coconut neera for shelf life extension was analysed. METHODS AND RESULTS The aliquots of fresh neera were frozen at -6 and -20°C. The microbial reduction and chemical qualities were analysed during storage days, and were compared with the control. The highest reduction in microbes was obtained at -20°C for lactic acid bacteria, yeast and total viable count. Moreover, the fluorescence cell staining and cell density analysis exhibited a decline at -20°C, however it showed higher at -6°C. At the end of 28 days, neera exhibited a pH of 5·37, total soluble solid of 14·0 °Brix and total acidity of 0·82 mg l-1 at -20°C. Besides, color, viscosity, total protein and ethanol showed a less difference with control and better sensory attribute up to 21 days at -20°C. CONCLUSIONS Frozen storage at -20°C resulted in a better inhibition of lactic acid bacteria, which preserves neera from the metabolic conversion. The physicochemical qualities of neera were preserved for a longer period when stored at -20°C than at atmospheric storage. SIGNIFICANCE AND IMPACT OF THE STUDY Frozen storage reduced microbial population and preserves the chemical properties with acceptable sensory attributes and increases the shelf life of coconut neera, making it fit for consumption.
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Affiliation(s)
- L Sukumaran
- Centre of Excellence in Nonthermal Processing, Indian Institute of Food Processing Technology, Ministry of Food Processing Industries, Government of India, Thanjavur, Tamil Nadu, India.,Affiliated to Bharathidasan University, Palkalaiperur, Tiruchirappalli, Tamil Nadu, India
| | - M Radhakrishnan
- Centre of Excellence in Nonthermal Processing, Indian Institute of Food Processing Technology, Ministry of Food Processing Industries, Government of India, Thanjavur, Tamil Nadu, India
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22
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Dudzinska W, Lubkowska A. Changes in the Concentration of Purine and Pyridine as a Response to Single Whole-Body Cryostimulation. Front Physiol 2021; 12:634816. [PMID: 33584352 PMCID: PMC7873528 DOI: 10.3389/fphys.2021.634816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 01/08/2021] [Indexed: 11/29/2022] Open
Abstract
To our knowledge, this is the first study in which we provide evidence that a single whole-body cryostimulation treatment leads to changes associated with erythrocyte energy metabolism. These changes are beneficial from the point of view of cellular bioenergetics, because they are associated with an increase in ATP concentration and erythrocyte energy potential expressed by an increase in the ATP/ADP and ATP/AMP ratios and the value of adenylate energy charge (AEC). In addition, as affected by cryogenic temperatures, there is a decrease in the concentration of purine catabolism products, i.e., inosine and hypoxanthine in the blood.
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Affiliation(s)
- Wioleta Dudzinska
- Institute of Biology, University of Szczecin, Szczecin, Poland.,Department of Functional Diagnostics and Physical Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Anna Lubkowska
- Department of Functional Diagnostics and Physical Medicine, Pomeranian Medical University in Szczecin, Szczecin, Poland
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23
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Shain DH, Novis PM, Cridge AG, Zawierucha K, Geneva AJ, Dearden PK. Five animal phyla in glacier ice reveal unprecedented biodiversity in New Zealand's Southern Alps. Sci Rep 2021; 11:3898. [PMID: 33594128 PMCID: PMC7887191 DOI: 10.1038/s41598-021-83256-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/01/2021] [Indexed: 11/24/2022] Open
Abstract
Glacier ice is an extreme environment in which most animals cannot survive. Here we report the colonization of high elevation, climate-threatened glaciers along New Zealand's southwestern coast by species of Arthropoda, Nematoda, Platyhelminthes, Rotifera and Tardigrada. Based on DNA barcoding and haplotype-inferred evidence for deep genetic variability, at least 12 undescribed species are reported, some of which have persisted in this niche habitat throughout the Pleistocene. These findings identify not only an atypical biodiversity hotspot but also highlight the adaptive plasticity of microinvertebrate Animalia.
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Affiliation(s)
- Daniel H Shain
- Biology Department, Rutgers The State University of New Jersey, Camden, NJ, 08103, USA.
| | - Philip M Novis
- Allan Herbarium, Manaaki Whenua-Landcare Research, Lincoln, 7608, New Zealand
| | - Andrew G Cridge
- Genomics Aotearoa and Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Krzysztof Zawierucha
- Department of Animal Taxonomy and Ecology, Adam Mickiewicz University in Poznań, 61-614, Poznań, Poland
| | - Anthony J Geneva
- Biology Department, Rutgers The State University of New Jersey, Camden, NJ, 08103, USA
| | - Peter K Dearden
- Genomics Aotearoa and Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
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24
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A comparative UHPLC-Q/TOF-MS-based eco-metabolomics approach reveals temperature adaptation of four Nepenthes species. Sci Rep 2020; 10:21861. [PMID: 33318532 PMCID: PMC7736350 DOI: 10.1038/s41598-020-78873-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/30/2020] [Indexed: 12/15/2022] Open
Abstract
Nepenthes, as the largest family of carnivorous plants, is found with an extensive geographical distribution throughout the Malay Archipelago, specifically in Borneo, Philippines, and Sumatra. Highland species are able to tolerate cold stress and lowland species heat stress. Our current understanding on the adaptation or survival mechanisms acquired by the different Nepenthes species to their climatic conditions at the phytochemical level is, however, limited. In this study, we applied an eco-metabolomics approach to identify temperature stressed individual metabolic fingerprints of four Nepenthes species: the lowlanders N. ampullaria, N. rafflesiana and N. northiana, and the highlander N. minima. We hypothesized that distinct metabolite regulation patterns exist between the Nepenthes species due to their adaptation towards different geographical and altitudinal distribution. Our results revealed not only distinct temperature stress induced metabolite fingerprints for each Nepenthes species, but also shared metabolic response and adaptation strategies. The interspecific responses and adaptation of N. rafflesiana and N. northiana likely reflected their natural habitat niches. Moreover, our study also indicates the potential of lowlanders, especially N. ampullaria and N. rafflesiana, to produce metabolites needed to deal with increased temperatures, offering hope for the plant genus and future adaption in times of changing climate.
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25
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Huo T, Zhao Y, Tang X, Zhao H, Ni S, Gao Q, Liu S. Metabolic acclimation of anammox consortia to decreased temperature. ENVIRONMENT INTERNATIONAL 2020; 143:105915. [PMID: 32652345 DOI: 10.1016/j.envint.2020.105915] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
Widespread application of anammox process has been primarily limited to the high sensitivity of anammox consortia to fluctuations of temperature. However, the metabolic acclimation of anammox consortia to decreased temperature remains unclear, which is the core of developing potential strategies for improving their low-temperature resistance. Here, we operated anammox reactors at 25 °C and 35 °C to explore the acclimation mechanism of anammox consortia in terms of metabolic responses and cross-feedings. Accordingly, we found that the adaptation of anammox consortia to ambient temperature (25 °C) was significantly linked to energy conservation strategy, resulting in decreased extracellular polymeric substance secretion, accumulation of ATP and amino acids. The expression patterns of cold shock proteins and core enzymes caused the apparent metabolic advantage of Candidatus Brocadia fulgida for acclimation to ambient temperature compared to other anammox species. Importantly, strengthened cross-feedings of amino acids, nitrite and glycine betaine benefited adaptation of anammox consortia to ambient temperature. Our work not only uncovers the temperature-adaptive mechanisms of anammox consortia, but also emphasizes the important role of metabolic cross-feeding in the temperature adaptation of microbial community.
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Affiliation(s)
- Tangran Huo
- Department of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yunpeng Zhao
- Department of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Xi Tang
- Department of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Huazhang Zhao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China
| | - Shouqing Ni
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Qiang Gao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China.
| | - Sitong Liu
- Department of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China.
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26
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Liu Y, Shen L, Zeng Y, Xing T, Xu B, Wang N. Genomic Insights of Cryobacterium Isolated From Ice Core Reveal Genome Dynamics for Adaptation in Glacier. Front Microbiol 2020; 11:1530. [PMID: 32765445 PMCID: PMC7381226 DOI: 10.3389/fmicb.2020.01530] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 06/12/2020] [Indexed: 11/30/2022] Open
Abstract
Glacier is the dominant cold habitat in terrestrial environments, providing a model ecosystem to explore extremophilic strategies and study early lives on Earth. The dominant form of life in glaciers is bacteria. However, little is known about past evolutionary processes that bacteria underwent during adaptation to the cryosphere and the connection of their genomic traits to environmental stressors. Aiming to test the hypothesis that bacterial genomic content and dynamics are driven by glacial environmental stressors, we compared genomes of 21 psychrophilic Cryobacterium strains, including 14 that we isolated from three Tibetan ice cores, to their mesophilic counterparts from the same family Microbacteriaceae of Actinobacteria. The results show that psychrophilic Cryobacterium underwent more dynamic changes in genome content, and their genomes have a significantly higher number of genes involved in stress response, motility, and chemotaxis than their mesophilic counterparts (P < 0.05). The phylogenetic birth-and-death model imposed on the phylogenomic tree indicates a vast surge in recent common ancestor of psychrophilic Cryobacterium (gained the greatest number of genes by 1,168) after the division of the mesophilic strain Cryobacterium mesophilum. The expansion in genome content brought in key genes primarily of the categories “cofactors, vitamins, prosthetic groups, pigments,” “monosaccharides metabolism,” and “membrane transport.” The amino acid substitution rates of psychrophilic Cryobacterium strains are two orders of magnitude lower than those in mesophilic strains. However, no significantly higher number of cold shock genes was found in psychrophilic Cryobacterium strains, indicating that multi-copy is not a key factor for cold adaptation in the family Microbacteriaceae, although cold shock genes are indispensable for psychrophiles. Extensive gene acquisition and low amino acid substitution rate might be the strategies of psychrophilic Cryobacterium to resist low temperature, oligotrophy, and high UV radiation on glaciers. The exploration of genome evolution and survival strategies of psychrophilic Cryobacterium deepens our understanding of bacterial cold adaptation.
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Affiliation(s)
- Yongqin Liu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Liang Shen
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Yonghui Zeng
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Tingting Xing
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Baiqing Xu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing, China
| | - Ninglian Wang
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing, China.,College of Urban and Environmental Science, Northwest University, Xi'an, China
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27
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Mukherjee R, Verma T, Nandi D, Umapathy S. Identification of a resonance Raman marker for cytochrome to monitor stress responses in Escherichia coli. Anal Bioanal Chem 2020; 412:5379-5388. [PMID: 32548767 DOI: 10.1007/s00216-020-02753-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/16/2020] [Accepted: 06/02/2020] [Indexed: 11/29/2022]
Abstract
Raman spectroscopy and resonance Raman spectroscopy are widely used to study bacteria and their responses to different environmental conditions. In the present study, the identification of a novel resonance Raman peak for Escherichia coli, recorded with 633 nm laser excitation is discussed. A peak at 740 cm-1 is observed exclusively with 633 nm excitation but not with 514 nm or 785 nm excitation. This peak is absent in the lag phase but appears in the log phase of bacterial growth. The intensity of the peak increases at high temperature (45 °C) compared with growth at low temperature (25 °C) or the physiological temperature (37 °C). Although osmotic stress lowered bacterial growth, the intensity of this peak was unaffected. However, treatment with chemical uncouplers of oxidative phosphorylation resulted in significantly lower intensity of this Raman band, indicating its possible involvement in respiration. Cytochromes, a component of bacterial respiration' can show resonance enhancement at 633 nm due to the presence of a shoulder in that region depending on the type and conformation of cytochrome. Therefore, the peak intensity was monitored in different genetic mutants of E. coli lacking cytochromes. This peak is absent in the Escherichia coli mutant lacking cydB, but not ccmE, demonstrating the contribution of cytochrome bd subunit II in the peak's origin. In future, this newly found cytochrome marker can be used for biochemical assessment of bacteria exposed to various conditions. Overall, this finding opens the scope for use of red laser excitation in resonance Raman in monitoring stress and respiration in bacteria. Graphical abstract.
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Affiliation(s)
- Ria Mukherjee
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Taru Verma
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Dipankar Nandi
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, Karnataka, 560012, India. .,Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India.
| | - Siva Umapathy
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India. .,Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, Karnataka, 560012, India. .,Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, Karnataka, 560012, India.
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28
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Lang SA, McIlroy P, Shain DH. Structural Evolution of the Glacier Ice Worm F o ATP Synthase Complex. Protein J 2020; 39:152-159. [PMID: 32112190 DOI: 10.1007/s10930-020-09889-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The segmented annelid worm, Mesenchytraeus solifugus, is a permanent resident of temperate, maritime glaciers in the Pacific northwestern region of North America, displaying atypically high intracellular ATP levels which have been linked to its unusual ability to thrive in hydrated glacier ice. We have shown previously that ice worms contain a highly basic, carboxy terminal extension on their ATP6 regulatory subunit, likely acquired by horizontal gene transfer from a microbial dietary source. Here we examine the full complement of F1F0 ATP synthase structural subunits with attention to non-conservative, ice worm-specific structural modifications. Our genomics analyses and molecular models identify putative proton shuttling domains on either side of the F0 hemichannel, which predictably function to enhance proton flow across the mitochondrial membrane. Other components of the ice worm ATP synthase complex have remained largely unchanged in the context of Metazoan evolution.
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Affiliation(s)
- Shirley A Lang
- Department of Biology, Haverford College, Haverford, PA, 19041, USA
| | - Patrick McIlroy
- Department of Biology and Center for Computational and Integrative Biology, Rutgers The State University of New Jersey, Camden, NJ, 08102, USA
| | - Daniel H Shain
- Department of Biology and Center for Computational and Integrative Biology, Rutgers The State University of New Jersey, Camden, NJ, 08102, USA.
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29
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Glycine Betaine Effect on Dormancy in Deinococcus sp. UDEC-P1 and Psychrobacter sp. UDEC-A5 Exposed to Hyperosmotic Stress. Curr Microbiol 2019; 76:1435-1442. [PMID: 31494741 DOI: 10.1007/s00284-019-01763-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 08/26/2019] [Indexed: 10/26/2022]
Abstract
Bacteria under stress increase the proportion of dormant cells to ensure their survival. Cold and osmotic stress are similar, because in both the availability of water is reduced. Glycine betaine (GB) is one of the most common osmoprotectants in bacteria and possesses cryoprotectant properties. Our aim was to determine whether GB modifies the proportion of dormant Deinococcus sp. UDEC-P1 and Psychrobacter sp. UDEC-A5 cells exposed to osmotic stress. Both bacterial strains were incubated in the presence of up to 1 M NaCl with or without GB. Active and dormant cells were evaluated by both spectrophotometric and flow cytometry analysis. Without GB, Deinococcus sp. UDEC-P1 grew in the presence of 0.05 M NaCl, but with 5 mM GB grew at 0.1 M NaCl. Psychrobacter sp. UDEC-A5 grew in the presence of up to 0.25 M NaCl, but with 5 mM GB grew at 0.5 M NaCl. Under osmotic stress, the proportion of dormant cells of Deinococcus sp. UDEC-P1 and Psychrobacter sp. UDEC-A5 increased significantly (about eightfold and fivefold, respectively). The addition of GB (5 mM) exerted a different effect on the two strains, since it avoided the entrance into the dormancy of Psychrobacter sp. UDEC-A5 cells, but not of Deinococcus sp. UDEC-P1 cells. Our results suggest that the effect of GB on bacterial metabolism is strain dependent. For bacteria in which GB avoids dormancy, such as Psychrobacter sp. UDEC-A5, it could be a "double-edged sword" by reducing the "seed bank" available to recover the active population when favorable conditions return.
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30
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Toni M, Angiulli E, Miccoli G, Cioni C, Alleva E, Frabetti F, Pizzetti F, Grassi Scalvini F, Nonnis S, Negri A, Tedeschi G, Maffioli E. Environmental temperature variation affects brain protein expression and cognitive abilities in adult zebrafish (Danio rerio): A proteomic and behavioural study. J Proteomics 2019; 204:103396. [DOI: 10.1016/j.jprot.2019.103396] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/30/2019] [Accepted: 05/24/2019] [Indexed: 11/26/2022]
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31
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Liu Q, Liu HC, Zhou YG, Xin YH. Microevolution and Adaptive Strategy of Psychrophilic Species Flavobacterium bomense sp. nov. Isolated From Glaciers. Front Microbiol 2019; 10:1069. [PMID: 31178833 PMCID: PMC6538692 DOI: 10.3389/fmicb.2019.01069] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022] Open
Abstract
Numerous mountain glaciers located on the Tibetan Plateau are inhabited by abundant microorganisms. The microorganisms on the glacier surface are exposed to the cold, barren, and high-ultraviolet radiation environments. Although the microbial community composition on glaciers has been revealed by high-throughput sequencing, little is known about the microevolution and adaptive strategy of certain bacterial populations. In this study, we used a polyphasic approach to determine the taxonomic status of 11 psychrophilic Flavobacterium strains isolated from glaciers on the Tibetan Plateau and performed a comparative genomic analysis. The phylogenetic tree based on the concatenated single-copy gene sequences showed the 11 strains clustered together, forming a distinct and novel clade in the genus Flavobacterium. The average nucleotide identity (ANI) values among these strains were higher than 96%. However, the values much lower than 90% between them and related species indicated that they represent a novel species and the name Flavobacterium bomense sp. nov. is proposed. The core and accessory genomes of strains in this new Flavobacterium species showed diverse distinct patterns of gene content and metabolism pathway. In order to infer the driving evolutionary forces of the core genomes, homologous recombination was found to contribute twice as much to nucleotide substitutions as mutations. A series of genes encoding proteins with known or predicted roles in cold adaptation were found in their genomes, for example, cold-shock protein, proteorhodopsin, osmoprotection, and membrane-related proteins. A comparative analysis of the group with optimal growth temperature (OGT) ≤ 20°C and the group with OGT > 20°C of the 32 Flavobacterium type strains and 11 new strains revealed multiple amino acid substitutions, including the decrease of the proline and glutamine content and the increase of the methionine and isoleucine content in the group with OGT ≤ 20°C, which may contribute to increased protein flexibility at low temperatures. Thus, this study discovered a novel Flavobacterium species in glaciers, which has high intraspecific diversity and multiple adaptation mechanisms that enable them to cope and thrive in extreme habitats.
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Affiliation(s)
- Qing Liu
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hong-Can Liu
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yu-Hua Xin
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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32
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Brown SP, Jumpponen A. Microbial Ecology of Snow Reveals Taxa-Specific Biogeographical Structure. MICROBIAL ECOLOGY 2019; 77:946-958. [PMID: 30868207 DOI: 10.1007/s00248-019-01357-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 03/06/2019] [Indexed: 06/09/2023]
Abstract
Snows that persist late into the growing season become colonized with numerous metabolically active microorganisms, yet underlying mechanisms of community assembly and dispersal remain poorly known. We investigated (Illumina MiSeq) snow-borne bacterial, fungal, and algal communities across a latitudinal gradient in Fennoscandia and inter-continental distribution between northern Europe and North America. Our data indicate that bacterial communities are ubiquitous regionally (across Fennoscandia), whereas fungal communities are regionally heterogeneous. Both fungi and bacteria are biogeographically heterogeneous inter-continentally. Snow algae, generally thought to occur in colorful algae blooms (red, green, or yellow) on the snow surface, are molecularly described here as an important component of snows even in absence of visible algal growth. This suggests that snow algae are a previously underestimated major biological component of visually uncolonized snows. In contrast to fungi and bacteria, algae exhibit no discernible inter-continental or regional community structure and exhibit little endemism. These results indicate that global and regional snow microbial communities and their distributions may be dictated by a combination of size-limited propagule dispersal potential and restrictions (bacteria and fungi) and homogenization of ecologically specialized taxa (snow algae) across the globe. These results are among the first to compare inter-continental snow microbial communities and highlight how poorly understood microbial communities in these threatened ephemeral ecosystems are.
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Affiliation(s)
- Shawn P Brown
- Department of Biological Sciences, The University of Memphis, Memphis, TN, 38152, USA.
| | - Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
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33
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Xie T, Pang R, Wu Q, Zhang J, Lei T, Li Y, Wang J, Ding Y, Chen M, Bai J. Cold Tolerance Regulated by the Pyruvate Metabolism in Vibrio parahaemolyticus. Front Microbiol 2019; 10:178. [PMID: 30787922 PMCID: PMC6372572 DOI: 10.3389/fmicb.2019.00178] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 01/22/2019] [Indexed: 11/13/2022] Open
Abstract
Vibrio parahaemolyticus is a common foodborne pathogen found in seafood, and represents a major threat to human health worldwide. Low-temperature storage is an important seafood processing method, but is not sufficient to completely eliminate the bacteria and avoid foodborne illness. To determine the mechanisms behind such cold tolerance, RNA-seq and iTRAQ analyses were first performed to obtain the global transcriptomic and proteomic patterns of frozen squid and clinical V. parahaemolyticus isolates under cold conditions. The integrated analysis revealed the modulation of multiple pathways such as the co-occurrence of down-regulated pyruvate metabolism and up-regulated fatty acid biosynthesis, which likely contribute to V. parahaemolyticus cold tolerance. Furthermore, we found that increasing concentrations of pyruvate can reduce the fatty acid content to influence V. parahaemolyticus growth in cold conditions. Thus, regulation of pyruvate concentration may be an effective method to control this seafood-borne pathogen.
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Affiliation(s)
- Tengfei Xie
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Rui Pang
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Qingping Wu
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Juemei Zhang
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Tao Lei
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Yanping Li
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Yu Ding
- Department of Food Science & Technology, Jinan University, Guangzhou, China
| | - Moutong Chen
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
| | - Jianlin Bai
- Guangdong Institute of Microbiology, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou, China
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34
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Köpnick C, Grübe M, Stock J, Senula A, Mock HP, Nagel M. Changes of soluble sugars and ATP content during DMSO droplet freezing and PVS3 droplet vitrification of potato shoot tips. Cryobiology 2018; 85:79-86. [PMID: 30257179 DOI: 10.1016/j.cryobiol.2018.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/05/2018] [Accepted: 09/19/2018] [Indexed: 12/13/2022]
Abstract
The potato's great genetic diversity needs to be maintained for future agricultural applications and can be preserved at ultra-low temperatures. To decipher detailed physiological processes, the aim of the study was to analyze the regrowth in 28 gene bank accessions and to reveal metabolite changes in a subset of four accessions that showed pronounced differences after shoot tip cryopreservation using DMSO droplet freezing and PVS3 droplet vitrification. Regrowth varied in all 28 genotypes ranging from 5% ('Kagiri') to 100% ('Karakter') and was higher after PVS3 droplet vitrification (71 ± 19%) than after cryopreservation using DMSO (54 ± 17%). Sucrose, glucose, and fructose were analyzed and showed significant increases after pre-culture in combination with PVS3 or DMSO and liquid nitrogen treatment and were reduced during regeneration. In contrast, adenosine triphosphate (ATP) reached its minimum concentration after cryoprotection and liquid nitrogen treatment and recovered most quickly after PVS3 droplet vitrification. A shortening of the explant pre-culture period reduced dramatically the regrowth after PVS3 vitrification. However, correlations between the shoot tip regrowth and sugar concentration were absent and significant at a low extent with ATP (r = 0.4, P < 0.01). Interestingly, several sub-cultivations of the donor plants from the previous stock affected negatively the regrowth. In conclusion, the cryopreservation protocol, genotypes, pre-culture period and number of sub-cultures affect the regrowth ability of explants, which was best estimated by the ATP concentration after low-temperature treatment. Due to the superior performance of PVS3, the routine potato cryopreservation at the Gatersleben gene bank was changed to PVS3 droplet vitrification.
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Affiliation(s)
- Claudia Köpnick
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Corrensstraße 3, 06466, Seeland, Germany
| | - Marion Grübe
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Corrensstraße 3, 06466, Seeland, Germany
| | - Johanna Stock
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Corrensstraße 3, 06466, Seeland, Germany
| | - Angelika Senula
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Corrensstraße 3, 06466, Seeland, Germany
| | - Hans-Peter Mock
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Corrensstraße 3, 06466, Seeland, Germany
| | - Manuela Nagel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Corrensstraße 3, 06466, Seeland, Germany.
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35
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Jones RM, Goordial JM, Orcutt BN. Low Energy Subsurface Environments as Extraterrestrial Analogs. Front Microbiol 2018; 9:1605. [PMID: 30072971 PMCID: PMC6058055 DOI: 10.3389/fmicb.2018.01605] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/27/2018] [Indexed: 11/13/2022] Open
Abstract
Earth's subsurface is often isolated from phototrophic energy sources and characterized by chemotrophic modes of life. These environments are often oligotrophic and limited in electron donors or electron acceptors, and include continental crust, subseafloor oceanic crust, and marine sediment as well as subglacial lakes and the subsurface of polar desert soils. These low energy subsurface environments are therefore uniquely positioned for examining minimum energetic requirements and adaptations for chemotrophic life. Current targets for astrobiology investigations of extant life are planetary bodies with largely inhospitable surfaces, such as Mars, Europa, and Enceladus. Subsurface environments on Earth thus serve as analogs to explore possibilities of subsurface life on extraterrestrial bodies. The purpose of this review is to provide an overview of subsurface environments as potential analogs, and the features of microbial communities existing in these low energy environments, with particular emphasis on how they inform the study of energetic limits required for life. The thermodynamic energetic calculations presented here suggest that free energy yields of reactions and energy density of some metabolic redox reactions on Mars, Europa, Enceladus, and Titan could be comparable to analog environments in Earth's low energy subsurface habitats.
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Affiliation(s)
| | | | - Beth N. Orcutt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
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36
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Bajerski F, Stock J, Hanf B, Darienko T, Heine-Dobbernack E, Lorenz M, Naujox L, Keller ERJ, Schumacher HM, Friedl T, Eberth S, Mock HP, Kniemeyer O, Overmann J. ATP Content and Cell Viability as Indicators for Cryostress Across the Diversity of Life. Front Physiol 2018; 9:921. [PMID: 30065659 PMCID: PMC6056685 DOI: 10.3389/fphys.2018.00921] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 06/25/2018] [Indexed: 11/30/2022] Open
Abstract
In many natural environments, organisms get exposed to low temperature and/or to strong temperature shifts. Also, standard preservation protocols for live cells or tissues involve ultradeep freezing in or above liquid nitrogen (-196°C or -150°C, respectively). To which extent these conditions cause cold- or cryostress has rarely been investigated systematically. Using ATP content as an indicator of the physiological state of cells, we found that representatives of bacteria, fungi, algae, plant tissue, as well as plant and human cell lines exhibited similar responses during freezing and thawing. Compared to optimum growth conditions, the cellular ATP content of most model organisms decreased significantly upon treatment with cryoprotectant and cooling to up to -196°C. After thawing and a longer period of regeneration, the initial ATP content was restored or even exceeded the initial ATP levels. To assess the implications of cellular ATP concentration for the physiology of cryostress, cell viability was determined in parallel using independent approaches. A significantly positive correlation of ATP content and viability was detected only in the cryosensitive algae Chlamydomonas reinhardtii SAG 11-32b and Chlorella variabilis NC64A, and in plant cell lines of Solanum tuberosum. When comparing mesophilic with psychrophilic bacteria of the same genera, and cryosensitive with cryotolerant algae, ATP levels of actively growing cells were generally higher in the psychrophilic and cryotolerant representatives. During exposure to ultralow temperatures, however, psychrophilic and cryotolerant species showed a decline in ATP content similar to their mesophilic or cryosensitive counterparts. Nevertheless, psychrophilic and cryotolerant species attained better culturability after freezing. Cellular ATP concentrations and viability measurements thus monitor different features of live cells during their exposure to ultralow temperatures and cryostress.
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Affiliation(s)
- Felizitas Bajerski
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Johanna Stock
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Benjamin Hanf
- Leibniz Institute for Natural Product Research and Infection Biology e.V. - Hans-Knöll-Institute (HKI), Jena, Germany.,Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Tatyana Darienko
- Experimental Phycology and Culture Collection of Algae, University of Göttingen (EPSAG), Göttingen, Germany
| | - Elke Heine-Dobbernack
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Maike Lorenz
- Experimental Phycology and Culture Collection of Algae, University of Göttingen (EPSAG), Göttingen, Germany
| | - Lisa Naujox
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - E R J Keller
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - H M Schumacher
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thomas Friedl
- Experimental Phycology and Culture Collection of Algae, University of Göttingen (EPSAG), Göttingen, Germany
| | - Sonja Eberth
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Mock
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Olaf Kniemeyer
- Leibniz Institute for Natural Product Research and Infection Biology e.V. - Hans-Knöll-Institute (HKI), Jena, Germany.,Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Lang SA, Shain DH. Atypical Evolution of the F 1F o Adenosine Triphosphate Synthase Regulatory ATP6 subunit in Glacier Ice Worms (Annelida: Clitellata: Mesenchytraeus). Evol Bioinform Online 2018; 14:1176934318788076. [PMID: 30022808 PMCID: PMC6047255 DOI: 10.1177/1176934318788076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 06/18/2018] [Indexed: 11/28/2022] Open
Abstract
The glacier ice worm, Mesenchytraeus solifugus, is among a few animals that reside permanently in glacier ice. Their adaptation to cold temperature has been linked to relatively high intracellular adenosine triphosphate (ATP) levels, which compensate for reductions in molecular motion at low physiological temperatures. Here, we show that ATP6-the critical regulatory subunit of the F1Fo-ATP synthase and primary target of mitochondrial disease-acquired an unprecedented histidine-rich, 18-amino acid carboxy-terminal extension, which counters the strong evolutionary trend of mitochondrial genome compaction. Furthermore, sequence analysis suggests that this insertion is not of metazoan origin, but rather is a product of horizontal gene transfer from a microbial dietary source, and may act as a proton shuttle to accelerate the rate of ATP synthesis.
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Affiliation(s)
- Shirley A Lang
- Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, USA
| | - Daniel H Shain
- Department of Biology, Rutgers, The State University of New Jersey, Camden, NJ, USA
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Bi Y, Zeng S, Zhang R, Diao Q, Tu Y. Effects of dietary energy levels on rumen bacterial community composition in Holstein heifers under the same forage to concentrate ratio condition. BMC Microbiol 2018; 18:69. [PMID: 29996759 PMCID: PMC6042446 DOI: 10.1186/s12866-018-1213-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/27/2018] [Indexed: 12/20/2022] Open
Abstract
Background The rumen bacterial community plays a critical role in feeds degradation and productivity. The effects of different forage to concentrate ratios on the ruminal microbial population structure have been studied extensively; however, research into changes in the ruminal bacterial community composition in heifers fed different energy level diets, with the same forage to concentrate ratio, has been very limited. The purpose of this study was to investigate the effects of different dietary energy levels, with the same forage to concentrate ratio, on ruminal bacterial community composition of heifers. Furthermore, we also determine the relationship between rumen bacteria and ruminal fermentation parameters. Results The 16S rRNA gene sequencing showed that, under the same forage to concentrate ratio of 50:50, an 8% difference in dietary energy level had no significant impact on the alpha diversity and the relative abundance of the major phyla and most of the major genera in heifers. In all the treatments groups, Firmicutes, Bacteroidetes, and Proteobacteria were the dominant phyla. Spearman correlation analysis between the relative abundances of the rumen bacteria at the genus level and the fermentation parameters showed that the relative abundances of Prevotella and BF311 were positively correlated with the ammonia nitrogen and butyrate concentrations, and these two genera were negatively correlated with the propionate and isovalerate concentrations, respectively, and the genus Bifidobacterium was positively correlated with the butyrate concentration and was negatively correlated with propionate and isovalerate concentration. The total volatile fatty acid concentration was positively correlated with BF311 abundances, and was negatively correlated with Trichococcus and Facklamia abundances. Conclusions Under the same forage to concentrate ratio condition of 50:50, an 8% difference in dietary energy levels had little impact on rumen bacterial community composition in heifers. The correlations between some genera of ruminal bacteria and the concentrations of volatile fatty acids and ammonia nitrogen might be indicative that the ruminal fermentation parameters are strongly influenced by the rumen bacterial community composition.
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Affiliation(s)
- Yanliang Bi
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, NO. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Shuqin Zeng
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, NO. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Rong Zhang
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, NO. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Qiyu Diao
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, NO. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Yan Tu
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, NO. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China.
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Bharudin I, Abu Bakar MF, Hashim NHF, Mat Isa MN, Alias H, Firdaus-Raih M, Md Illias R, Najimudin N, Mahadi NM, Abu Bakar FD, Abdul Murad AM. Unravelling the adaptation strategies employed by Glaciozyma antarctica PI12 on Antarctic sea ice. MARINE ENVIRONMENTAL RESEARCH 2018; 137:169-176. [PMID: 29598997 DOI: 10.1016/j.marenvres.2018.03.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/09/2018] [Accepted: 03/19/2018] [Indexed: 06/08/2023]
Abstract
Glaciozyma antarctica PI12, is a psychrophilic yeast isolated from Antarctic sea. In this work, Expressed Sequence Tags (EST) from cells exposed to three different temperatures; 15 °C, 0 °C and -12 °C were generated to identify genes associated with cold adaptation. A total of 5376 clones from each library were randomly picked and sequenced. Comparative analyses from the resulting ESTs in each condition identified several groups of genes required for cold adaptation. Additionally, 319 unique transcripts that encoded uncharacterised functions were identified in the -12 °C library and are currently unique to G. antarctica. Gene expression analysis using RT-qPCR revealed two of the unknown genes to be up-regulated at -12 °C compared to 0 °C and 15 °C. These findings further contribute to the collective knowledge into G. antarctica cold adaptation and as a resource for understanding the ecological and physiological tolerance of psychrophilic microbes in general.
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Affiliation(s)
- Izwan Bharudin
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia.
| | | | - Noor Haza Fazlin Hashim
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia
| | - Mohd Noor Mat Isa
- Malaysia Genome Institute, Jalan Bangi Lama, 43000, Kajang, Selangor, Malaysia
| | - Halimah Alias
- Malaysia Genome Institute, Jalan Bangi Lama, 43000, Kajang, Selangor, Malaysia
| | - Mohd Firdaus-Raih
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia; Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia
| | - Rosli Md Illias
- Department of Biosciences Engineering, Faculty of Chemical & Natural Resources Engineering, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Nazalan Najimudin
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Nor Muhammad Mahadi
- Malaysia Genome Institute, Jalan Bangi Lama, 43000, Kajang, Selangor, Malaysia
| | - Farah Diba Abu Bakar
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia
| | - Abdul Munir Abdul Murad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia
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Hashim NHF, Mahadi NM, Illias RM, Feroz SR, Abu Bakar FD, Murad AMA. Biochemical and structural characterization of a novel cold-active esterase-like protein from the psychrophilic yeast Glaciozyma antarctica. Extremophiles 2018; 22:607-616. [DOI: 10.1007/s00792-018-1021-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 03/11/2018] [Indexed: 02/04/2023]
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Jousse C, Dalle C, Canet I, Lagrée M, Traïkia M, Lyan B, Mendes C, Sancelme M, Amato P, Delort AM. Metabolomic study of the response to cold shock in a strain of Pseudomonas syringae isolated from cloud water. Metabolomics 2017; 14:11. [PMID: 30830325 DOI: 10.1007/s11306-017-1295-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 11/07/2017] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Active microorganisms have been recently discovered in clouds, thus demonstrating the capacity of microorganisms to exist in harsh environments, including exposure to UV and oxidants, osmotic and cold shocks, etc. It is important to understand how microorganisms respond to and survive such stresses at the metabolic level. OBJECTIVES The objective of this work is to assess metabolome modulation in a strain of Pseudomonas syringae isolated from cloud water and facing temperature downshift from 17 to 5 °C by identifying key molecules and pathways of the response/adaptation to cold shock. METHODS Bacterial extracts from suspensions of cells grown at 17 °C and further incubated in microcosms at 5 and 17 °C to mimic cloud conditions were analysed by combining LC-MS and NMR; the results were evaluated in comparison to similar suspensions kept at constant temperature. The differences in the metabolome profiles were deciphered using multivariate statistics (PLS-DA). RESULTS Key cold shock biomarkers were observed, including cryoprotectants (trehalose, glucose, glycerol, carnitine, glutamate), antioxidants (glutathione and carnitine) and their precursors, alkaloids (bellendine and slaframine) and metabolites involved in energy metabolism (ATP, carbohydrates). Furthermore, new short peptides (nine dipeptides and a tetrapeptide) were found that have no known function. CONCLUSIONS This study shows that in response to cold temperatures, Pseudomonas syringae PDD-32b-74 demonstrates numerous metabolism modifications to counteract the impacts of low temperatures.
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Affiliation(s)
- Cyril Jousse
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
- Université Clermont Auvergne - INRA, MetaboHUB/Plateforme d'exploration du métabolisme, Clermont-Ferrand, France
| | - Céline Dalle
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
- Université Clermont Auvergne - INRA, MetaboHUB/Plateforme d'exploration du métabolisme, Clermont-Ferrand, France
| | - Isabelle Canet
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
| | - Marie Lagrée
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
- Université Clermont Auvergne - INRA, MetaboHUB/Plateforme d'exploration du métabolisme, Clermont-Ferrand, France
| | - Mounir Traïkia
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
- Université Clermont Auvergne - INRA, MetaboHUB/Plateforme d'exploration du métabolisme, Clermont-Ferrand, France
| | - Bernard Lyan
- Université Clermont Auvergne - INRA, UNH, 63000, Clermont-Ferrand, France
- Université Clermont Auvergne - INRA, MetaboHUB/Plateforme d'exploration du métabolisme, Clermont-Ferrand, France
| | - Cédric Mendes
- Université Clermont Auvergne - INRA, MetaboHUB/Plateforme d'exploration du métabolisme, Clermont-Ferrand, France
| | - Martine Sancelme
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
| | - Pierre Amato
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
| | - Anne-Marie Delort
- Université Clermont Auvergne - CNRS - SIGMA-Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France.
- Université Clermont Auvergne - INRA, MetaboHUB/Plateforme d'exploration du métabolisme, Clermont-Ferrand, France.
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Genome content, metabolic pathways and biotechnological potential of the psychrophilic Arctic bacterium Psychrobacter sp. DAB_AL43B, a source and a host of novel Psychrobacter-specific vectors. J Biotechnol 2017; 263:64-74. [PMID: 28919459 DOI: 10.1016/j.jbiotec.2017.09.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 09/10/2017] [Accepted: 09/14/2017] [Indexed: 01/06/2023]
Abstract
Psychrobacter sp. DAB_AL43B, isolated from ornithogenic soil collected on the Arctic island of Spitsbergen, is a newly sequenced psychrophilic strain susceptible to conjugation and electrotransformation. Its genome consists of a circular chromosome (3.3 Mb) and four plasmids (4.4-6.4kb). In silico genome mining and microarray-based phenotypic analysis were performed to describe the metabolic potential of this strain and identify possible biotechnological applications. Metabolic reconstruction indicated that DAB_AL43B prefers low-molecular-weight carboxylates and amino acids as carbon and energy sources. Genetic determinants of heavy-metal resistance, anthracene degradation and possible aerobic denitrification were also identified. Comparative analyses revealed a relatively close relationship between DAB_AL43B and other sequenced Psychrobacter species. In addition, the plasmids of this strain were used as the basis for the construction of Escherichia coli-Psychrobacter spp. shuttle vectors. Taken together, the results of this work suggest that DAB_AL43B is a promising candidate as a new model strain for studies on Psychrobacter spp.
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Qi M, Bilbao S, Forouhar E, Kandeel F, Al-Abdullah IH. Encompassing ATP, DNA, insulin, and protein content for quantification and assessment of human pancreatic islets. Cell Tissue Bank 2017; 19:77-85. [PMID: 28916910 PMCID: PMC5829119 DOI: 10.1007/s10561-017-9659-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/11/2017] [Indexed: 12/11/2022]
Abstract
Islet transplantation has made major progress to treat patients with type 1 diabetes. Islet mass and quality are critically important to ensure successful transplantation. Currently, islet status is evaluated using insulin secretion, oxygen consumption rate, or adenosine triphosphate (ATP) measurement. These parameters are evaluated independently and do not effectively predict islet status post-transplant. Therefore, assessing human pancreatic islets by encompassing ATP, DNA, insulin, and protein content from a single tissue sample would serve as a better predictor for islet status. In this study, a single step procedure for extracting ATP, DNA, insulin, and protein content from human pancreatic islets was described and the biomolecule contents were quantified. Additionally, different mathematical calculations integrating total ATP, DNA, insulin, and protein content were randomly tested under various conditions to predict islet status. The results demonstrated that the ATP assay was efficient and the biomolecules were effectively quantified. Furthermore, the mathematical formula we developed could be optimized to predict islet status. In conclusion, our results indicate a proof-of-concept that a simple logarithmic formula can predict overall islet status for various conditions when total islet ATP, DNA, insulin, and protein content are simultaneously assessed from a single tissue sample.
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Affiliation(s)
- Meirigeng Qi
- Department of Translational Research and Cellular Therapeutics, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA, 91010, USA
| | - Shiela Bilbao
- Department of Translational Research and Cellular Therapeutics, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA, 91010, USA
| | - Elena Forouhar
- Department of Translational Research and Cellular Therapeutics, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA, 91010, USA
| | - Fouad Kandeel
- Department of Translational Research and Cellular Therapeutics, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA, 91010, USA
| | - Ismail H Al-Abdullah
- Department of Translational Research and Cellular Therapeutics, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA, 91010, USA.
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Garcia-Lopez E, Cid C. Glaciers and Ice Sheets As Analog Environments of Potentially Habitable Icy Worlds. Front Microbiol 2017; 8:1407. [PMID: 28804477 PMCID: PMC5532398 DOI: 10.3389/fmicb.2017.01407] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/11/2017] [Indexed: 01/09/2023] Open
Abstract
Icy worlds in the solar system and beyond have attracted a remarkable attention as possible habitats for life. The current consideration about whether life exists beyond Earth is based on our knowledge of life in terrestrial cold environments. On Earth, glaciers and ice sheets have been considered uninhabited for a long time as they seemed too hostile to harbor life. However, these environments are unique biomes dominated by microbial communities which maintain active biochemical routes. Thanks to techniques such as microscopy and more recently DNA sequencing methods, a great biodiversity of prokaryote and eukaryote microorganisms have been discovered. These microorganisms are adapted to a harsh environment, in which the most extreme features are the lack of liquid water, extremely cold temperatures, high solar radiation and nutrient shortage. Here we compare the environmental characteristics of icy worlds, and the environmental characteristics of terrestrial glaciers and ice sheets in order to address some interesting questions: (i) which are the characteristics of habitability known for the frozen worlds, and which could be compatible with life, (ii) what are the environmental characteristics of terrestrial glaciers and ice sheets that can be life-limiting, (iii) What are the microbial communities of prokaryotic and eukaryotic microorganisms that can live in them, and (iv) taking into account these observations, could any of these planets or satellites meet the conditions of habitability? In this review, the icy worlds are considered from the point of view of astrobiological exploration. With the aim of determining whether icy worlds could be potentially habitable, they have been compared with the environmental features of glaciers and ice sheets on Earth. We also reviewed some field and laboratory investigations about microorganisms that live in analog environments of icy worlds, where they are not only viable but also metabolically active.
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Affiliation(s)
| | - Cristina Cid
- Microbial Evolution Laboratory, Centro de Astrobiología (Consejo Superior de Investigaciones Cientificas-Instituto Nacional de Técnica Aeroespacial)Madrid, Spain
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Bore EK, Apostel C, Halicki S, Kuzyakov Y, Dippold MA. Microbial Metabolism in Soil at Subzero Temperatures: Adaptation Mechanisms Revealed by Position-Specific 13C Labeling. Front Microbiol 2017; 8:946. [PMID: 28611748 PMCID: PMC5447017 DOI: 10.3389/fmicb.2017.00946] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/11/2017] [Indexed: 11/13/2022] Open
Abstract
Although biogeochemical models designed to simulate carbon (C) and nitrogen (N) dynamics in high-latitude ecosystems incorporate extracellular parameters, molecular and biochemical adaptations of microorganisms to freezing remain unclear. This knowledge gap hampers estimations of the C balance and ecosystem feedback in high-latitude regions. To analyze microbial metabolism at subzero temperatures, soils were incubated with isotopomers of position-specifically 13C-labeled glucose at three temperatures: +5 (control), -5, and -20°C. 13C was quantified in CO2, bulk soil, microbial biomass, and dissolved organic carbon (DOC) after 1, 3, and 10 days and also after 30 days for samples at -20°C. Compared to +5°C, CO2 decreased 3- and 10-fold at -5 and -20°C, respectively. High 13C recovery in CO2 from the C-1 position indicates dominance of the pentose phosphate pathway at +5°C. In contrast, increased oxidation of the C-4 position at subzero temperatures implies a switch to glycolysis. A threefold higher 13C recovery in microbial biomass at -5 than +5°C points to synthesis of intracellular compounds such as glycerol and ethanol in response to freezing. Less than 0.4% of 13C was recovered in DOC after 1 day, demonstrating complete glucose uptake by microorganisms even at -20°C. Consequently, we attribute the fivefold higher extracellular 13C in soil than in microbial biomass to secreted antifreeze compounds. This suggests that with decreasing temperature, intracellular antifreeze protection is complemented by extracellular mechanisms to avoid cellular damage by crystallizing water. The knowledge of sustained metabolism at subzero temperatures will not only be useful for modeling global C dynamics in ecosystems with periodically or permanently frozen soils, but will also be important in understanding and controlling the adaptive mechanisms of food spoilage organisms.
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Affiliation(s)
- Ezekiel K. Bore
- Department of Agricultural Soil Science, University of GöttingenGöttingen, Germany
| | - Carolin Apostel
- Department of Agricultural Soil Science, University of GöttingenGöttingen, Germany
- Department of Soil Science of Temperate Ecosystems, University of GöttingenGöttingen, Germany
| | - Sara Halicki
- Department of Agricultural Soil Science, University of GöttingenGöttingen, Germany
| | - Yakov Kuzyakov
- Department of Agricultural Soil Science, University of GöttingenGöttingen, Germany
- Department of Soil Science of Temperate Ecosystems, University of GöttingenGöttingen, Germany
- Institute of Environmental Sciences, Kazan Federal UniversityKazan, Russia
| | - Michaela A. Dippold
- Department of Agricultural Soil Science, University of GöttingenGöttingen, Germany
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Koh HY, Park H, Lee JH, Han SJ, Sohn YC, Lee SG. Proteomic and transcriptomic investigations on cold-responsive properties of the psychrophilic Antarctic bacterium Psychrobacter sp. PAMC 21119 at subzero temperatures. Environ Microbiol 2016; 19:628-644. [PMID: 27750393 DOI: 10.1111/1462-2920.13578] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 10/12/2016] [Indexed: 11/28/2022]
Abstract
Psychrobacter sp. PAMC 21119, isolated from Antarctic permafrost soil, grows and proliferates at subzero temperatures. However, its major mechanism of cold adaptation regulation remains poorly understood. We investigated the transcriptomic and proteomic responses of this species to cold temperatures by comparing profiles at -5°C and 20°C to understand how extreme microorganisms survive under subzero conditions. We found a total of 2,906 transcripts and 584 differentially expressed genes (≥ twofold, P <0.005) by RNA-seq. Genes for translation, ribosomal structure and biogenesis were upregulated, and lipid transport and metabolism was downregulated at low temperatures. A total of 60 protein spots (≥ 1.8 fold, P < 0.005) showed differential expression on two-dimensional gel electrophoresis and the proteins were identified by mass spectrometry. The most prominent upregulated proteins in response to cold were involved in metabolite transport, protein folding and membrane fluidity. Proteins involved in energy production and conversion, and heme protein synthesis were downregulated. Moreover, isoform exchange of cold-shock proteins was detected at both temperatures. Interestingly, pathways for acetyl-CoA metabolism, putrescine synthesis and amino acid metabolism were upregulated. This study highlights some of the strategies and different physiological states that Psychrobacter sp. PAMC 21119 has developed to adapt to the cold environment in Antarctica.
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Affiliation(s)
- Hye Yeon Koh
- Unit of Polar Genomics Korea Polar Research Institute, Incheon, South Korea.,Department of Marine Molecular Biotechnology, Gangneung-Wonju National University, Gangneung, South Korea
| | - Hyun Park
- Unit of Polar Genomics Korea Polar Research Institute, Incheon, South Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, South Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics Korea Polar Research Institute, Incheon, South Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, South Korea
| | - Se Jong Han
- Unit of Polar Genomics Korea Polar Research Institute, Incheon, South Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, South Korea
| | - Young Chang Sohn
- Department of Marine Molecular Biotechnology, Gangneung-Wonju National University, Gangneung, South Korea
| | - Sung Gu Lee
- Unit of Polar Genomics Korea Polar Research Institute, Incheon, South Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, South Korea
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47
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Okotrub KA, Surovtsev NV. Redox State of Cytochromes in Frozen Yeast Cells Probed by Resonance Raman Spectroscopy. Biophys J 2016; 109:2227-34. [PMID: 26636934 DOI: 10.1016/j.bpj.2015.10.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 10/23/2015] [Accepted: 10/26/2015] [Indexed: 12/20/2022] Open
Abstract
Cryopreservation is a well-established technique used for the long-term storage of biological materials whose biological activity is effectively stopped under low temperatures (suspended animation). Since most biological methods do not work in a low-temperature frozen environment, the mechanism and details of the depression of cellular activity in the frozen state remain largely uncharacterized. In this work, we propose, to our knowledge, a new approach to study the downregulation of the redox activity of cytochromes b and c in freezing yeast cells in a contactless, label-free manner. Our approach is based on cytochrome photobleaching effects observed in the resonance Raman spectra of live cells. Photoinduced and native redox reactions that contributed to the photobleaching rate were studied over a wide temperature range (from -173 to +25 °C). We found that ice formation influences both the rate of cytochrome redox reactions and the balance between the reduced and oxidized cytochromes. We demonstrate that the temperature dependence of native redox reaction rates can be well described by the thermal activation law with an apparent energy of 32.5 kJ/mol, showing that the redox reaction rate is ∼10(15) times slower at liquid nitrogen temperature than at room temperature.
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Affiliation(s)
- Konstantin A Okotrub
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk, Russia
| | - Nikolay V Surovtsev
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia.
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48
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Resilience of sulfate-reducing granular sludge against temperature, pH, oxygen, nitrite, and free nitrous acid. Appl Microbiol Biotechnol 2016; 100:8563-72. [DOI: 10.1007/s00253-016-7652-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/24/2016] [Accepted: 05/27/2016] [Indexed: 01/25/2023]
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49
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Harrison JP, Dobinson L, Freeman K, McKenzie R, Wyllie D, Nixon SL, Cockell CS. Aerobically respiring prokaryotic strains exhibit a broader temperature-pH-salinity space for cell division than anaerobically respiring and fermentative strains. J R Soc Interface 2016; 12:0658. [PMID: 26354829 DOI: 10.1098/rsif.2015.0658] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Biological processes on the Earth operate within a parameter space that is constrained by physical and chemical extremes. Aerobic respiration can result in adenosine triphosphate yields up to over an order of magnitude higher than those attained anaerobically and, under certain conditions, may enable microbial multiplication over a broader range of extremes than other modes of catabolism. We employed growth data published for 241 prokaryotic strains to compare temperature, pH and salinity values for cell division between aerobically and anaerobically metabolizing taxa. Isolates employing oxygen as the terminal electron acceptor exhibited a considerably more extensive three-dimensional phase space for cell division (90% of the total volume) than taxa using other inorganic substrates or organic compounds as the electron acceptor (15% and 28% of the total volume, respectively), with all groups differing in their growth characteristics. Understanding the mechanistic basis of these differences will require integration of research into microbial ecology, physiology and energetics, with a focus on global-scale processes. Critical knowledge gaps include the combined impacts of diverse stress parameters on Gibbs energy yields and rates of microbial activity, interactions between cellular energetics and adaptations to extremes, and relating laboratory-based data to in situ limits for cell division.
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Affiliation(s)
- Jesse P Harrison
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, King's Buildings, Edinburgh EH9 3FD, UK
| | - Luke Dobinson
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, King's Buildings, Edinburgh EH9 3FD, UK
| | - Kenneth Freeman
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, King's Buildings, Edinburgh EH9 3FD, UK
| | - Ross McKenzie
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, King's Buildings, Edinburgh EH9 3FD, UK
| | - Dale Wyllie
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, King's Buildings, Edinburgh EH9 3FD, UK
| | - Sophie L Nixon
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, King's Buildings, Edinburgh EH9 3FD, UK
| | - Charles S Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, King's Buildings, Edinburgh EH9 3FD, UK
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50
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Global metabolomic responses of Nitrosomonas europaea 19718 to cold stress and altered ammonia feeding patterns. Appl Microbiol Biotechnol 2015; 100:1843-1852. [DOI: 10.1007/s00253-015-7095-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/04/2015] [Accepted: 10/13/2015] [Indexed: 10/22/2022]
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