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Mercogliano M, De Chiara S, De Nicola A, Cardellini J, Montis C, Yakimov MM, La Cono V, Crisafi F, Silipo A, Berti D, Milano G, Molinaro A, Di Lorenzo F. Bucking the trend: understanding lipopolysaccharide structure and outer membrane dynamics in cold-adapted Pseudomonas isolated from Enigma Lake, Antarctica. Chem Sci 2024:d4sc05116e. [PMID: 39328195 PMCID: PMC11421494 DOI: 10.1039/d4sc05116e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Accepted: 09/17/2024] [Indexed: 09/28/2024] Open
Abstract
Cold environments are predominant over the Earth and are inhabited by bacteria able to cope with a series of simultaneous environmental pressures. Gram-negative species of the Pseudomonas genus are the predominant ones isolated from cold habitats, making them an excellent model for studying the mechanisms of bacterial adaptation to the most extreme habitats on our planet. Here we focused on the lipopolysaccharide (LPS) structure and the outer membrane dynamics of Pseudomonas sp. EW#7, a strain isolated from Enigma Lake in Antarctica where, among other extreme characteristics, water temperature can reach 0.4 °C. We show that near-zero growth temperature mostly affects the LPS lipid A component. An uncommon tendency of decreasing lipid A secondary hydroxylation while increasing its phosphorylation degree was observed. This resulted in a faster lateral diffusion of lipid chains in the membrane and therefore in an enhancement of its fluctuations that guarantee membrane integrity and flexibility.
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Affiliation(s)
- Marcello Mercogliano
- Department of Chemical Science, University of Naples Federico II Via Cinthia, 4 Naples 80126 Italy
| | - Stefania De Chiara
- Department of Chemical Science, University of Naples Federico II Via Cinthia, 4 Naples 80126 Italy
| | - Antonio De Nicola
- Cineca Casalecchio di Reno (BO) 40033 Italy
- Research Center for Organic Electronics (ROEL), Yamagata University 4-3-16 Jonan Yonezawa Yamagata 992-8510 Japan
| | - Jacopo Cardellini
- Consorzio Interuniversitario Per Lo Sviluppo Dei Sistemi A Grande Interfase Via Della Lastruccia 3 Firenze 50019 Italy
- Dipartimento Di Chimica "Ugo Schiff", Università Degli Studi di Firenze Via Della Lastruccia 3 Firenze 50019 Italy
| | - Costanza Montis
- Consorzio Interuniversitario Per Lo Sviluppo Dei Sistemi A Grande Interfase Via Della Lastruccia 3 Firenze 50019 Italy
- Dipartimento Di Chimica "Ugo Schiff", Università Degli Studi di Firenze Via Della Lastruccia 3 Firenze 50019 Italy
| | - Mikhail M Yakimov
- Institute of Polar Sciences, National Research Council of Italy (ISP-CNR) Via S. Raineri 4 Messina 98122 Italy
| | - Violetta La Cono
- Institute of Polar Sciences, National Research Council of Italy (ISP-CNR) Via S. Raineri 4 Messina 98122 Italy
| | - Francesca Crisafi
- Institute of Polar Sciences, National Research Council of Italy (ISP-CNR) Via S. Raineri 4 Messina 98122 Italy
| | - Alba Silipo
- Department of Chemical Science, University of Naples Federico II Via Cinthia, 4 Naples 80126 Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore Via Gaetano Salvatore 486 Napoli 80145 Italy
| | - Debora Berti
- Consorzio Interuniversitario Per Lo Sviluppo Dei Sistemi A Grande Interfase Via Della Lastruccia 3 Firenze 50019 Italy
- Dipartimento Di Chimica "Ugo Schiff", Università Degli Studi di Firenze Via Della Lastruccia 3 Firenze 50019 Italy
| | - Giuseppe Milano
- Department of Chemical, Material and Production Engineering, University of Naples Federico II Piazzale V. Tecchio, 80 Naples 80125 Italy
| | - Antonio Molinaro
- Department of Chemical Science, University of Naples Federico II Via Cinthia, 4 Naples 80126 Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore Via Gaetano Salvatore 486 Napoli 80145 Italy
- Department of Chemistry, School of Science, Osaka University 1-1 Osaka University Machikaneyama Toyonaka Osaka 560-0043 Japan
| | - Flaviana Di Lorenzo
- Department of Chemical Science, University of Naples Federico II Via Cinthia, 4 Naples 80126 Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore Via Gaetano Salvatore 486 Napoli 80145 Italy
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2
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Arora J, Chauhan A, Ranjan A, Rajput VD, Minkina T, Zhumbei AI, Kumari A, Jindal T, Prasad R. Degradation of SDS by psychrotolerant Staphylococcus saprophyticus and Bacillus pumilus isolated from Southern Ocean water samples. Braz J Microbiol 2024; 55:1507-1519. [PMID: 38468117 PMCID: PMC11153461 DOI: 10.1007/s42770-024-01294-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 02/26/2024] [Indexed: 03/13/2024] Open
Abstract
Bioremediation of surfactants in water bodies holds significant ecological importance as they are contaminants of emerging concern posing substantial threats to the aquatic environment. Microbes exhibiting special ability in terms of bioremediation of contaminants have always been reported to thrive in extraordinary environmental conditions that can be extreme in terms of temperature, lack of nutrients, and salinity. Therefore, in the present investigation, a total of 46 bacterial isolates were isolated from the Indian sector of the Southern Ocean and screened for degradation of sodium dodecyl sulphate (SDS). Further, two Gram-positive psychrotolerant bacterial strains, ASOI-01 and ASOI-02 were identified with significant SDS degradation potential. These isolates were further studied for growth optimization under different environmental conditions. The strains were characterized as Staphylococcus saprophyticus and Bacillus pumilus based on morphological, biochemical, and molecular (16S RNA gene) characteristics. The study reports 88.9% and 93.4% degradation of SDS at a concentration of 100 mgL-1, at 20 °C, and pH 7 by S. saprophyticus ASOI-01 and B. pumilus ASOI-02, respectively. The experiments were also conducted in wastewater samples where a slight reduction in degradation efficiency was observed with strains ASOI-01 and ASOI-02 exhibiting 76.83 and 64.93% degradation of SDS respectively. This study infers that these bacteria can be used for the bioremediation of anionic surfactants from water bodies and establishes the potential of extremophilic microbes for the utilization of sustainable wastewater management.
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Affiliation(s)
- Jayati Arora
- Amity Institute of Environmental Science, Amity University, Noida, Uttar Pradesh, India
| | - Abhishek Chauhan
- Amity Institute of Environmental Toxicology, Safety and Management, Amity University, Noida, Uttar Pradesh, India
| | - Anuj Ranjan
- Amity Institute of Environmental Toxicology, Safety and Management, Amity University, Noida, Uttar Pradesh, India.
- Academy of Biology and Biotechnology, Southern Federal University, Stachki 194/1, Rostov-On-Don, Russia.
| | - Vishnu D Rajput
- Academy of Biology and Biotechnology, Southern Federal University, Stachki 194/1, Rostov-On-Don, Russia
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, Stachki 194/1, Rostov-On-Don, Russia
| | - Anton Igorevich Zhumbei
- Academy of Biology and Biotechnology, Southern Federal University, Stachki 194/1, Rostov-On-Don, Russia
| | - Arpna Kumari
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-Ku, Tokyo, Japan
| | - Tanu Jindal
- Amity Institute of Environmental Toxicology, Safety and Management, Amity University, Noida, Uttar Pradesh, India
| | - Ram Prasad
- Department of Botany, Mahatma Gandhi Central University, Motihari, 845401, Bihar, India.
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Xu H, Xu D, Liu Y. Molecular Biology Applications of Psychrophilic Enzymes: Adaptations, Advantages, Expression, and Prospective. Appl Biochem Biotechnol 2024:10.1007/s12010-023-04810-5. [PMID: 38183603 DOI: 10.1007/s12010-023-04810-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2023] [Indexed: 01/08/2024]
Abstract
Psychrophilic enzymes are primarily produced by microorganisms from extremely low-temperature environments which are known as psychrophiles. Their high efficiency at low temperatures and easy heat inactivation property have attracted extensive attention from various food and industrial bioprocesses. However, the application of these enzymes in molecular biology is still limited. In a previous review, the applications of psychrophilic enzymes in industries such as the detergent additives, the food additives, the bioremediation, and the pharmaceutical medicine, and cosmetics have been discussed. In this review, we discuss the main cold adaptation characteristics of psychrophiles and psychrophilic enzymes, as well as the relevant information on different psychrophilic enzymes in molecular biology. We summarize the mining and screening methods of psychrophilic enzymes. We finally recap the expression of psychrophilic enzymes. We aim to provide a reference process for the exploration and expression of new generation of psychrophilic enzymes.
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Affiliation(s)
- Hu Xu
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Dawei Xu
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Yongqin Liu
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China.
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
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Robicheau BM, Tolman J, Rose S, Desai D, LaRoche J. Marine nitrogen-fixers in the Canadian Arctic Gateway are dominated by biogeographically distinct noncyanobacterial communities. FEMS Microbiol Ecol 2023; 99:fiad122. [PMID: 37951299 PMCID: PMC10656255 DOI: 10.1093/femsec/fiad122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/30/2023] [Accepted: 11/09/2023] [Indexed: 11/13/2023] Open
Abstract
We describe diazotrophs present during a 2015 GEOTRACES expedition through the Canadian Arctic Gateway (CAG) using nifH metabarcoding. In the less studied Labrador Sea, Bradyrhizobium sp. and Vitreoscilla sp. nifH variants were dominant, while in Baffin Bay, a Stutzerimonas stutzeri variant was dominant. In comparison, the Canadian Arctic Archipelago (CAA) was characterized by a broader set of dominant variants belonging to Desulfobulbaceae, Desulfuromonadales, Arcobacter sp., Vibrio spp., and Sulfuriferula sp. Although dominant diazotrophs fell within known nifH clusters I and III, only a few of these variants were frequently recovered in a 5-year weekly nifH times series in the coastal NW Atlantic presented herein, notably S. stutzeri and variants belonging to Desulfobacterales and Desulfuromonadales. In addition, the majority of dominant Arctic nifH variants shared low similarity (< 92% nucleotide identities) to sequences in a global noncyanobacterial diazotroph catalog recently compiled by others. We further detected UCYN-A throughout the CAG at low-levels using quantitative-PCR assays. Temperature, depth, salinity, oxygen, and nitrate were most strongly correlated to the Arctic diazotroph diversity observed, and we found a stark division between diazotroph communities of the Labrador Sea versus Baffin Bay and the CAA, hence establishing that a previously unknown biogeographic community division can occur for diazotrophs in the CAG.
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Affiliation(s)
- Brent M Robicheau
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Jennifer Tolman
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Sonja Rose
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Dhwani Desai
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, B3H 4R2, Canada
- Department of Pharmacology, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Julie LaRoche
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, B3H 4R2, Canada
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Borhani S, Arab SS. Investigation of thermal stability characteristic in family A DNA polymerase - A theoretical study. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 182:15-25. [PMID: 37187447 DOI: 10.1016/j.pbiomolbio.2023.05.003] [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: 11/17/2022] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 05/17/2023]
Abstract
DNA polymerases create complementary DNA strands in living cells and are crucial to genome transmission and maintenance. These enzymes possess similar human right-handed folds which contain thumb, fingers, and palm subdomains and contribute to polymerization activities. These enzymes are classified into seven evolutionary families, A, B, C, D, X, Y, and RT, based on amino acid sequence analysis and biochemical characteristics. Family A DNA polymerases exist in an extended range of organisms including mesophilic, thermophilic, and hyper-thermophilic bacteria, participate in DNA replication and repair, and have a broad application in molecular biology and biotechnology. In this study, we attempted to detect factors that play a role in the thermostability properties of this family member despite their remarkable similarities in structure and function. For this purpose, similarities and differences in amino acid sequences, structure, and dynamics of these enzymes have been inspected. Our results demonstrated that thermophilic and hyper-thermophilic enzymes have more charged, aromatic, and polar residues than mesophilic ones and consequently show further electrostatic and cation-pi interactions. In addition, in thermophilic enzymes, aliphatic residues tend to position in buried states more than mesophilic enzymes. These residues within their aliphatic parts increase hydrophobic core packing and therefore enhance the thermostability of these enzymes. Furthermore, a decrease in thermophilic cavities volumes assists in the protein compactness enhancement. Moreover, molecular dynamic simulation results revealed that increasing temperature impacts mesophilic enzymes further than thermophilic ones that reflect on polar and aliphatic residues surface area and hydrogen bonds changes.
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Affiliation(s)
- Seddigheh Borhani
- Biophysics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Seyed Shahriar Arab
- Biophysics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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Collins T, Feller G. Psychrophilic enzymes: strategies for cold-adaptation. Essays Biochem 2023; 67:701-713. [PMID: 37021674 DOI: 10.1042/ebc20220193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/17/2023] [Accepted: 03/27/2023] [Indexed: 04/07/2023]
Abstract
Psychrophilic organisms thriving at near-zero temperatures synthesize cold-adapted enzymes to sustain cell metabolism. These enzymes have overcome the reduced molecular kinetic energy and increased viscosity inherent to their environment and maintained high catalytic rates by development of a diverse range of structural solutions. Most commonly, they are characterized by a high flexibility coupled with an intrinsic structural instability and reduced substrate affinity. However, this paradigm for cold-adaptation is not universal as some cold-active enzymes with high stability and/or high substrate affinity and/or even an unaltered flexibility have been reported, pointing to alternative adaptation strategies. Indeed, cold-adaptation can involve any of a number of a diverse range of structural modifications, or combinations of modifications, depending on the enzyme involved, its function, structure, stability, and evolutionary history. This paper presents the challenges, properties, and adaptation strategies of these enzymes.
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Affiliation(s)
- Tony Collins
- Department of Biology, Center of Molecular and Environmental Biology (CBMA), University of Minho, 4710-057 Braga, Portugal
| | - Georges Feller
- Department of Life Sciences, Laboratory of Biochemistry, Center for Protein Engineering-InBioS, University of Liège, 4000 Liège, Belgium
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Chauhan M, Kimothi A, Sharma A, Pandey A. Cold adapted Pseudomonas: ecology to biotechnology. Front Microbiol 2023; 14:1218708. [PMID: 37529326 PMCID: PMC10388556 DOI: 10.3389/fmicb.2023.1218708] [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: 05/08/2023] [Accepted: 06/26/2023] [Indexed: 08/03/2023] Open
Abstract
The cold adapted microorganisms, psychrophiles/psychrotolerants, go through several modifications at cellular and biochemical levels to alleviate the influence of low temperature stress conditions. The low temperature environments depend on these cold adapted microorganisms for various ecological processes. The ability of the microorganisms to function in cold environments depends on the strategies directly associated with cell metabolism, physicochemical constrains, and stress factors. Pseudomonas is one among such group of microorganisms which is predominant in cold environments with a wide range of ecological and biotechnological applications. Bioformulations of Pseudomonas spp., possessing plant growth promotion and biocontrol abilities for application under low temperature environments, are well documented. Further, recent advances in high throughput sequencing provide essential information regarding the prevalence of Pseudomonas in rhizospheres and their role in plant health. Cold adapted species of Pseudomonas are also getting recognition for their potential in biodegradation and bioremediation of environmental contaminants. Production of enzymes and bioactive compounds (primarily as an adaptation mechanism) gives way to their applications in various industries. Exopolysaccharides and various biotechnologically important enzymes, produced by cold adapted species of Pseudomonas, are making their way in food, textiles, and pharmaceuticals. The present review, therefore, aims to summarize the functional versatility of Pseudomonas with particular reference to its peculiarities along with the ecological and biotechnological applications.
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Affiliation(s)
- Mansi Chauhan
- Department of Microbiology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, India
| | - Ayushi Kimothi
- Department of Microbiology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, India
| | - Avinash Sharma
- National Centre for Cell Science, Pune, Maharashtra, India
| | - Anita Pandey
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, India
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8
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Lee H, Cho YJ, Cho A, Kim OS. Environmental Adaptation of Psychrophilic Bacteria Subtercola spp. Isolated from Various Cryospheric Habitats. J Microbiol 2023; 61:663-672. [PMID: 37615929 DOI: 10.1007/s12275-023-00068-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 08/25/2023]
Abstract
Subtercola boreus K300T is a novel psychrophilic strain that was isolated from permanently cold groundwater in Finland and has also been found in several places in Antarctica including lake, soil, and rocks. We performed genomic and transcriptomic analyses of 5 strains from Antarctica and a type strain to understand their adaptation to different environments. Interestingly, the isolates from rocks showed a low growth rate and smaller genome size than strains from the other isolation sources (lake, soil, and groundwater). Based on these habitat-dependent characteristics, the strains could be classified into two ecotypes, which showed differences in energy production, signal transduction, and transcription in the clusters of orthologous groups of proteins (COGs) functional category. In addition, expression pattern changes revealed differences in metabolic processes, including uric acid metabolism, DNA repair, major facilitator superfamily (MFS) transporters, and xylose degradation, depending on the nutritional status of their habitats. These findings provide crucial insights into the environmental adaptation of bacteria, highlighting genetic diversity and regulatory mechanisms that enable them to thrive in the cryosphere.
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Affiliation(s)
- Hanbyul Lee
- Division of Polar Life Science, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Yong-Joon Cho
- Division of Polar Life Science, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
- Department of Molecular Bioscience, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Ahnna Cho
- Division of Polar Life Science, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Ok-Sun Kim
- Division of Polar Life Science, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.
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9
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Identification of phenotypic and genotypic properties and cold adaptive mechanisms of novel freeze–thaw stress-resistant strain Pseudomonas mandelii from Antarctica. Polar Biol 2023. [DOI: 10.1007/s00300-023-03114-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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10
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Rabbani G, Ahmad E, Ahmad A, Khan RH. Structural features, temperature adaptation and industrial applications of microbial lipases from psychrophilic, mesophilic and thermophilic origins. Int J Biol Macromol 2023; 225:822-839. [PMID: 36402388 DOI: 10.1016/j.ijbiomac.2022.11.146] [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: 06/10/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
Microbial lipases are very prominent biocatalysts because of their ability to catalyze a wide variety of reactions in aqueous and non-aqueous media. Here microbial lipases from different origins (psychrophiles, mesophiles, and thermophiles) have been reviewed. This review emphasizes an update of structural diversity in temperature adaptation and industrial applications, of psychrophilic, mesophilic, and thermophilic lipases. The microbial origins of lipases are logically dynamic, proficient, and also have an extensive range of industrial uses with the manufacturing of altered molecules. It is therefore of interest to understand the molecular mechanisms of adaptation to temperature in occurring lipases. However, lipases from extremophiles (psychrophiles, and thermophiles) are widely used to design biotransformation reactions with higher yields, fewer byproducts, or useful side products and have been predicted to catalyze those reactions also, which otherwise are not possible with the mesophilic lipases. Lipases as a multipurpose biological catalyst have given a favorable vision in meeting the needs of several industries such as biodiesel, foods, and drinks, leather, textile, detergents, pharmaceuticals, and medicals.
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Affiliation(s)
- Gulam Rabbani
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202 002, India; Department of Medical Biotechnology, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongbuk 38541, Republic of Korea.
| | - Ejaz Ahmad
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, United States of America
| | - Abrar Ahmad
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202 002, India.
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Matinja AI, Kamarudin NHA, Leow ATC, Oslan SN, Ali MSM. Cold-Active Lipases and Esterases: A Review on Recombinant Overexpression and Other Essential Issues. Int J Mol Sci 2022; 23:ijms232315394. [PMID: 36499718 PMCID: PMC9740821 DOI: 10.3390/ijms232315394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/21/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022] Open
Abstract
Cold environments characterised by diverse temperatures close to or below the water freezing point dominate about 80% of the Earth's biosphere. One of the survival strategies adopted by microorganisms living in cold environments is their expression of cold-active enzymes that enable them to perform an efficient metabolic flux at low temperatures necessary to thrive and reproduce under those constraints. Cold-active enzymes are ideal biocatalysts that can reduce the need for heating procedures and improve industrial processes' quality, sustainability, and cost-effectiveness. Despite their wide applications, their industrial usage is still limited, and the major contributing factor is the lack of complete understanding of their structure and cold adaptation mechanisms. The current review looked at the recombinant overexpression, purification, and recent mechanism of cold adaptation, various approaches for purification, and three-dimensional (3D) crystal structure elucidation of cold-active lipases and esterase.
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Affiliation(s)
- Adamu Idris Matinja
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Department of Biochemistry, Faculty of Science, Bauchi State University, Gadau 751105, Nigeria
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Enzyme Technology and X-ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Correspondence:
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12
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Yu X, Zhang W, Zhang G, Wu Y, Wu S, Tian M, Ding W, Bahadur A, Chen T, Liu G. Arthrobacter antioxidans sp. nov., a blue pigment-producing species isolated from Mount Everest. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748457 DOI: 10.1099/ijsem.0.005624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacteria in the genus Arthrobacter have been found in extreme environments, e.g. glaciers, brine and mural paintings. Here, we report the discovery of a novel pink-coloured bacterium, strain QL17T, capable of producing an extracellular water-soluble blue pigment. The bacterium was isolated from the soil of the East Rongbuk Glacier of Mt. Everest, China. 16S rRNA gene sequence analysis showed that strain QL17T was most closely related to the species Arthrobacter bussei KR32 T. However, compared to A.bussei KR32T and the next closest relatives, the new species demonstrates considerable phylogenetic distance at the whole-genome level, with an average nucleotide identity of <85 % and inferred DNA-DNA hybridization of <30 %. Polyphasic taxonomy results support our conclusion that strain QL17T represents a novel species of the genus Arthrobacter. Strain QL17T had the highest tolerance to hydrogen peroxide at 400 mM. Whole-genome sequencing of strain QL17T revealed the presence of numerous cold-adaptation, antioxidation and UV resistance-associated genes, which are related to adaptation to the extreme environment of Mt. Everest. Results of this study characterized a novel psychrotolerant Arthrobacter species, for which the name Arthrobacter antioxidans sp. nov. is proposed. The type strain is QL17T (GDMCC 1.2948T=JCM 35246T).
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Affiliation(s)
- Xue Yu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu province, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu province, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China.,State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu province, PR China
| | - Yujie Wu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China.,State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu province, PR China
| | - Shiyu Wu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
| | - Mao Tian
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China.,State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu province, PR China
| | - Wei Ding
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Ali Bahadur
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China.,State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu province, PR China
| | - Tuo Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China.,State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu province, PR China
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu province, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
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13
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Antarctic aldehyde dehydrogenase from Flavobacterium PL002 as a potent catalyst for acetaldehyde determination in wine. Sci Rep 2022; 12:17301. [PMID: 36243887 PMCID: PMC9569350 DOI: 10.1038/s41598-022-22289-8] [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: 08/10/2022] [Accepted: 10/12/2022] [Indexed: 01/10/2023] Open
Abstract
Latest solutions in biotechnologies and biosensing targeted cold-active extremozymes. Analysis of acetaldehyde as a relevant quality indicator of wine is one example of application that could benefit from using low-temperatures operating catalysts. In search of novel aldehyde dehydrogenases (ALDH) with high stability and activity at low temperatures, the recombinant S2-ALDH from the Antarctic Flavobacterium PL002 was obtained by cloning and expression in Escherichia coli BL21(DE3). Structural and phylogenetic analyses revealed strong protein similarities (95%) with psychrophilic homologs, conserved active residues and structural elements conferring enzyme flexibility. Arrhenius plot revealed a conformational shift at 30 °C, favoring catalysis (low activation energy) at lower temperatures. In addition to a broad substrate specificity with preference for acetaldehyde (Km = 1.88 mM), this enzyme showed a high tolerance for ethanol (15%) and several salts and chelators (an advantage for wine analysis), while being sensitive to mercury (I50 = 1.21 µM). The neutral optimal pH (7.5) and the stability up to 40 °C and after lyophilization represent major assets for developing S2-ALDH-based sensors. An enzymatic electrochemical assay was developed for acetaldehyde detection in wines with proven accuracy in comparison with the reference spectrophotometric method, thus evidencing the potential of S2-ALDH as effective biocatalyst for industry and biosensing.
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14
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Stimmler P, Priemé A, Elberling B, Goeckede M, Schaller J. Arctic soil respiration and microbial community structure driven by silicon and calcium. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156152. [PMID: 35609699 DOI: 10.1016/j.scitotenv.2022.156152] [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: 12/17/2021] [Revised: 03/18/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Global warming is most pronounced in the Arctic region. Greenhouse gas (GHG) release from Arctic soils increase due to global warming. By this, the Arctic may change from currently being a carbon sink to a future source. To improve accurate predictions of future GHG release from Arctic soils, it is important to unravel factors controlling both the microbial community structure and activity. Soil microbial activity is important for Arctic greenhouse gas production, but depends on soil conditions such as salinity being increased by calcium (Ca) and decreased by amorphous silica (Si) potentially enhancing water availability. In the Arctic, climate changes may alter salinity by changing Si and Ca concentrations upon permafrost thaw as a result of global warming with Si potentially decreasing and Ca potentially increasing salinity. Here, we show that higher Si concentration increased and higher Ca concentrations decreased the microbial CO2 production for both a salt-poor and a salt-rich soil from Greenland. In the salt-rich soil, Si amendment increased CO2 production and the abundance of gram-negative bacteria. However, the bacterial community became dominated by spore-forming gram-positive Firmicutes and Actinobacteria. The CO2 release from soils was directly affected by the abundance of bacteria and fungi, and their community structure. Our results highlight the importance of the soil Si and Ca concentration on organic carbon turnover by strongly changing microbial abundance and community structure, with consequences for CO2 release in the Arctic. Consequently, Ca and Si and their relation to Arctic soil microbial community structure has to be considered when estimating pan-Arctic carbon budgets.
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Affiliation(s)
- Peter Stimmler
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, Germany.
| | - Anders Priemé
- Department of Biology, University of Copenhagen, 1350 Copenhagen, Denmark; Center for Permafrost, Department of Geosciences and Natural Resource Management, University of Copenhagen, 1350 Copenhagen, Denmark.
| | - Bo Elberling
- Center for Permafrost, Department of Geosciences and Natural Resource Management, University of Copenhagen, 1350 Copenhagen, Denmark; Department of Geosciences and Natural Resource Management, University of Copenhagen, 1350 Copenhagen, Denmark.
| | | | - Joerg Schaller
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, Germany.
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15
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Sivasankar P, Poongodi S, Sivakumar K, Al-Qahtani WH, Arokiyaraj S, Jothiramalingam R. Exogenous production of cold-active cellulase from polar Nocardiopsis sp. with increased cellulose hydrolysis efficiency. Arch Microbiol 2022; 204:218. [PMID: 35333982 DOI: 10.1007/s00203-022-02830-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 03/08/2022] [Indexed: 12/01/2022]
Abstract
The present work was designed to isolate and characterise the actinobacteria in the Polar Front region of the Southern Ocean waters and species of Nocardiopsis and Streptomyces were identified. Among those, the psychrophilic actinobacterium, Nocardiopsis dassonvillei PSY13 was found to have good cellulolytic activity and it was further studied for the production and characterisation of cold-active cellulase enzyme. The latter was found to have a specific activity of 6.36 U/mg and a molar mass of 48 kDa with a 22.9-fold purification and 5% recovery at an optimum pH of 7.5 and a temperature of 10 °C. Given the importance of psychrophilic actinobacteria, N. dassonvillei PSY13 can be further exploited for its benefits, meaning that the Southern Ocean harbours biotechnologically important microorganisms that can be further explored for versatile biotechnological and industrial applications.
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Affiliation(s)
- Palaniappan Sivasankar
- Water Supply and Bioeconomy Division, Faculty of Environmental Engineering and Energy, Poznan University of Technology, Berdychowo 4, 60-965, Poznan, Poland. .,Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai, 608 502, Tamil Nadu, India.
| | - Subramaniam Poongodi
- Department of Microbiology, Shri Sakthikailassh Women's College, Salem, 636 003, Tamil Nadu, India
| | - Kannan Sivakumar
- Centre of Advanced Study in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai, 608 502, Tamil Nadu, India
| | - Wahidah H Al-Qahtani
- Department of Food Sciences & Nutrition, College of Food & Agriculture Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Selvaraj Arokiyaraj
- Department of Food Science and Biotechnology, Sejong University, Seoul, South Korea
| | - R Jothiramalingam
- Department of Food Sciences & Nutrition, College of Food & Agriculture Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
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16
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Mondini A, Anwar MZ, Ellegaard-Jensen L, Lavin P, Jacobsen CS, Purcarea C. Heat Shock Response of the Active Microbiome From Perennial Cave Ice. Front Microbiol 2022; 12:809076. [PMID: 35360653 PMCID: PMC8960993 DOI: 10.3389/fmicb.2021.809076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/28/2021] [Indexed: 11/13/2022] Open
Abstract
Ice caves constitute the newly investigated frozen and secluded model habitats for evaluating the resilience of ice-entrapped microbiomes in response to climate changes. This survey identified the total and active prokaryotic and eukaryotic communities from millennium-old ice accumulated in Scarisoara cave (Romania) using Illumina shotgun sequencing of the ribosomal RNA (rRNA) and messenger RNA (mRNA)-based functional analysis of the metatranscriptome. Also, the response of active microbiome to heat shock treatment mimicking the environmental shift during ice melting was evaluated at both the taxonomic and metabolic levels. The putatively active microbial community was dominated by bacterial taxa belonging to Proteobacteria and Bacteroidetes, which are highly resilient to thermal variations, while the scarcely present archaea belonging to Methanomicrobia was majorly affected by heat shock. Among eukaryotes, the fungal rRNA community was shared between the resilient Chytridiomycota and Blastocladiomycota, and the more sensitive Ascomycota and Basidiomycota taxa. A complex microeukaryotic community highly represented by Tardigrada and Rotifera (Metazoa), Ciliophora and Cercozoa (Protozoa), and Chlorophyta (Plantae) was evidenced for the first time in this habitat. This community showed a quick reaction to heat shock, followed by a partial recovery after prolonged incubation at 4°C due to possible predation processes on the prokaryotic cluster. Analysis of mRNA differential gene expression revealed the presence of an active microbiome in the perennial ice from the Scarisoara cave and associated molecular mechanisms for coping with temperature variations by the upregulation of genes involved in enzyme recovery, energy storage, carbon and nitrogen regulation, and cell motility. This first report on the active microbiome embedded in perennial ice from caves and its response to temperature stress provided a glimpse into the impact of glaciers melting and the resilience mechanisms in this habitat, contributing to the knowledge on the functional role of active microbes in frozen environments and their response to climatic changes.
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Affiliation(s)
- Antonio Mondini
- Department of Microbiology, Institute of Biology, Bucharest, Romania
| | - Muhammad Zohaib Anwar
- Department of Environmental Science, Aarhus University, RISØ Campus, Roskilde, Denmark
- Center for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Lea Ellegaard-Jensen
- Department of Environmental Science, Aarhus University, RISØ Campus, Roskilde, Denmark
| | - Paris Lavin
- Centre of Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Carsten Suhr Jacobsen
- Department of Environmental Science, Aarhus University, RISØ Campus, Roskilde, Denmark
| | - Cristina Purcarea
- Department of Microbiology, Institute of Biology, Bucharest, Romania
- *Correspondence: Cristina Purcarea,
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18
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Abirami B, Radhakrishnan M, Kumaran S, Wilson A. Impacts of global warming on marine microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 791:147905. [PMID: 34126492 DOI: 10.1016/j.scitotenv.2021.147905] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 04/26/2021] [Accepted: 05/16/2021] [Indexed: 06/12/2023]
Abstract
Global warming in ocean ecosystems alters temperature, acidification, oxygen content, circulation, stratification, and nutrient inputs. Microorganisms play a dominant role in global biogeochemical cycles crucial for a planet's sustainability. Since microbial communities are highly dependent on the temperature factor, fluctuations in the same will lead to adverse effects on the microbial community organization. Throughout the Ocean, increase in evaporation rates causes the surface mixed layer to become shallower. This intensified stratification inhibits vertical transport of nutrient supplies. Such density driven processes will decrease oxygen solubility in surface waters leading to significant decrease of oxygen from future Ocean. Metabolism and diversity of microbes along with ocean biogeochemistry will be at great risk due to global warming and its related effects. As a response to the changes in temperature, alteration in the distribution of phytoplankta communities is observed all over the planet, creating changes in the primary production of the ocean causing massive impact on the biosphere. Marine microbial communities try to adapt to the changing ocean environmental conditions by responding with biogeographic range shifts, community structure modifications, and adaptive evolution. Persistence of this climate change on ocean ecosystems, in future, will pose serious threat to the metabolism and distribution of marine microbes leading to fluctuations in the biogeochemical cycles thereby affecting the overall ecosystem functioning. Genomics plays an important role in marine microbial research by providing tools to study the association between environment and organisms. The ecological and genomic perspectives of marine microbes are being investigated to design effective models to understand their physiology and evolution in a changing ocean. Mesocosm/microcosm experimental studies and field studies are in the need of the hour to evaluate the impact of climate shifts on microbial genesis.
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Affiliation(s)
- Baskaran Abirami
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Manikkam Radhakrishnan
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Subramanian Kumaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Aruni Wilson
- Sathyabama Institute of Science and Technology, Chennai 600119, Tamil Nadu, India; School of Medicine, Loma Linda University, CA, USA; Musculoskeletal Disease Research Laboratory, US Department of Veteran Affairs, Loma Linda, CA, USA.
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19
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Evaluation of Biocompatibility and Antagonistic Properties of Microorganisms Isolated from Natural Sources for Obtaining Biofertilizers Using Microalgae Hydrolysate. Microorganisms 2021; 9:microorganisms9081667. [PMID: 34442746 PMCID: PMC8401578 DOI: 10.3390/microorganisms9081667] [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: 06/26/2021] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 12/04/2022] Open
Abstract
Determination of the biocompatibility of microorganisms isolated from natural sources (Kemerovo Oblast—Kuzbass) resulted in the creation of three microbial consortia based on the isolated strains: consortium I (Bacillus pumilus, Pediococcus damnosus, and Pediococcus pentosaceus), consortium II (Acetobacter aceti, Pseudomonas chlororaphis, and Streptomyces parvus), and consortium III (Amycolatopsis sacchari, Bacillus stearothermophilus; Streptomyces thermocarboxydus; and Streptomyces thermospinisporus). The nutrient media composition for the cultivation of each of the three studied microbial consortia, providing the maximum increase in biomass, was selected: consortium I, nutrient medium 11; consortium II, nutrient medium 13; for consortium III, nutrient medium 16. Consortia I and II microorganisms were cultured at 5–25 °C, and consortium III at 50–70 °C. Six types of psychrophilic microorganisms (P. pentosaceus, P. chlororaphis, P. damnosus, B. pumilus, A. aceti, and S. parvus) and four types of thermophilic microorganisms (B. stearothermophilus, S. thermocarboxydus, S. thermospinisporus, and A. sacchari) were found to have high antagonistic activity against the tested pathogenic strains (A. faecalis, B. cinerea, E. carotovora, P. aeruginosa, P. fluorescens, R. stolonifera, X. vesicatoria. pv. Vesicatoria, and E. aphidicola). The introduction of microalgae hydrolyzate increased the concentration of microorganisms by 5.23 times in consortium I, by 4.66 times in consortium II, by 6.6 times in consortium III. These data confirmed the efficiency (feasibility) of introducing microalgae hydrolyzate into the biofertilizer composition.
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20
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First Insights into the Microbiology of Three Antarctic Briny Systems of the Northern Victoria Land. DIVERSITY 2021. [DOI: 10.3390/d13070323] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Different polar environments (lakes and glaciers), also in Antarctica, encapsulate brine pools characterized by a unique combination of extreme conditions, mainly in terms of high salinity and low temperature. Since 2014, we have been focusing our attention on the microbiology of brine pockets from three lakes in the Northern Victoria Land (NVL), lying in the Tarn Flat (TF) and Boulder Clay (BC) areas. The microbial communities have been analyzed for community structure by next generation sequencing, extracellular enzyme activities, metabolic potentials, and microbial abundances. In this study, we aim at reconsidering all available data to analyze the influence exerted by environmental parameters on the community composition and activities. Additionally, the prediction of metabolic functions was attempted by the phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) tool, highlighting that prokaryotic communities were presumably involved in methane metabolism, aromatic compound biodegradation, and organic compound (proteins, polysaccharides, and phosphates) decomposition. The analyzed cryoenvironments were different in terms of prokaryotic diversity, abundance, and retrieved metabolic pathways. By the analysis of DNA sequences, common operational taxonomic units ranged from 2.2% to 22.0%. The bacterial community was dominated by Bacteroidetes. In both BC and TF brines, sequences of the most thermally tolerant and methanogenic Archaea were detected, some of them related to hyperthermophiles.
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21
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Kim J, Lee AH, Chang W. Manipulation of Unfrozen Water Retention for Enhancing Petroleum Hydrocarbon Biodegradation in Seasonally Freezing and Frozen Soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:9172-9180. [PMID: 34156830 DOI: 10.1021/acs.est.0c07502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Manipulating the retention of unfrozen water in freezing contaminated soil to achieve prolonged bioremediation in cold climates remains unformulated. This freezing-induced biodegradation experiment shows how nutrient and zeolite amendments affect unfrozen water retention and hydrocarbon biodegradation in field-aged, petroleum-contaminated soils undergoing seasonal freezing. During soil freezing at a site-specific rate (4 to -10 °C and -0.2 °C/d), the effect of nutrients was predominant during early freezing (4 to -5 °C), alleviating the abrupt soil-freezing stress near the freezing-point depressions, elevating alkB1 gene-harboring populations, and enhancing hydrocarbon biodegradation. Subsequently, the effect of increased unfrozen water retention associated with added zeolite surface areas was critical in extending hydrocarbon biodegradation to the frozen phase (-5 to -10 °C). A series of soil-freezing characteristic curves with empirical α-values (soil-freezing index) were constructed for the tested soils and shown alongside representative curves for clays to sands, indicating correlations between α-values and nutrient concentrations (soil electrical conductivity), zeolite addition (surface area), and hydrocarbon biodegradation. Heavier hydrocarbons (F3: C16-C34) notably biodegraded in all treated soils (22-37% removal), as confirmed by biomarker-based analyses (17α(H),21β(H)-hopane), whereas lighter hydrocarbons were not biodegraded. Below 0 °C, finer-grained soils (high α-values) can be biostimulated more readily than coarser-grained soils (low α-values).
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Affiliation(s)
- Jihun Kim
- Department of Civil, Geological, and Environmental Engineering, University of Saskatchewan, 57 Campus Drive, Engineering Building, Saskatoon, Saskatchewan S7N 5A9, Canada
| | - Aslan Hwanhwi Lee
- Department of Civil, Geological, and Environmental Engineering, University of Saskatchewan, 57 Campus Drive, Engineering Building, Saskatoon, Saskatchewan S7N 5A9, Canada
| | - Wonjae Chang
- Department of Civil, Geological, and Environmental Engineering, University of Saskatchewan, 57 Campus Drive, Engineering Building, Saskatoon, Saskatchewan S7N 5A9, Canada
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22
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Fructose-Based Production of Short-Chain-Length and Medium-Chain-Length Polyhydroxyalkanoate Copolymer by Arctic Pseudomonas sp. B14-6. Polymers (Basel) 2021; 13:polym13091398. [PMID: 33925903 PMCID: PMC8123457 DOI: 10.3390/polym13091398] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 04/19/2021] [Accepted: 04/22/2021] [Indexed: 02/06/2023] Open
Abstract
Arctic bacteria employ various mechanisms to survive harsh conditions, one of which is to accumulate carbon and energy inside the cell in the form of polyhydroxyalkanoate (PHA). Whole-genome sequencing of a new Arctic soil bacterium Pseudomonas sp. B14-6 revealed two PHA-production-related gene clusters containing four PHA synthase genes (phaC). Pseudomonas sp. B14-6 produced poly(6% 3-hydroxybutyrate-co-94% 3-hydroxyalkanoate) from various carbon sources, containing short-chain-length PHA (scl-PHA) and medium-chain-length PHA (mcl-PHA) composed of various monomers analyzed by GC-MS, such as 3-hydroxybutyrate, 3-hydroxyhexanoate, 3-hydroxyoctanoate, 3-hydroxydecanoate, 3-hydroxydodecenoic acid, 3-hydroxydodecanoic acid, and 3-hydroxytetradecanoic acid. By optimizing the PHA production media, we achieved 34.6% PHA content using 5% fructose, and 23.7% PHA content using 5% fructose syrup. Differential scanning calorimetry of the scl-co-mcl PHA determined a glass transition temperature (Tg) of 15.3 °C, melting temperature of 112.8 °C, crystallization temperature of 86.8 °C, and 3.82% crystallinity. In addition, gel permeation chromatography revealed a number average molecular weight of 3.6 × 104, weight average molecular weight of 9.1 × 104, and polydispersity index value of 2.5. Overall, the novel Pseudomonas sp. B14-6 produced a polymer with high medium-chain-length content, low Tg, and low crystallinity, indicating its potential use in medical applications.
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Del Moral Á, Garrido-Benavent I, Durán J, Lehmann JR, Rodríguez A, Heiðmarsson S, de Los Ríos A. Are recently deglaciated areas at both poles colonised by the same bacteria? FEMS Microbiol Lett 2021; 368:6122588. [PMID: 33507249 DOI: 10.1093/femsle/fnab011] [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: 10/06/2020] [Accepted: 01/25/2021] [Indexed: 01/05/2023] Open
Abstract
Polar glacier forefields offer an unprecedented framework for studying community assembly processes in regions that are geographically and climatically isolated. Through amplicon sequence variant (ASV) inference, we compared the composition and structure of soil bacterial communities from glacier forefields in Iceland and Antarctica to assess overlap between communities and the impact of established cryptogamic covers on the uniqueness of their taxa. These pioneer microbial communities were found to share only 8% of ASVs and each taxonomic group's contribution to the shared ASV data subset was heterogeneous and independent of their relative abundance. Although the presence of ASVs specific to one glacier forefield and/or different cryptogam cover values confirms the existence of habitat specialist bacteria, our data show that the influence of cryptogams on the edaphic bacterial community structure also varied also depending on the taxonomic group. Hence, the establishment of distinct cryptogamic covers is probably not the only factor driving the uniqueness of bacterial communities at both poles. The structure of bacterial communities colonising deglaciated areas seems also conditioned by lineage-specific limitations in their dispersal capacity and/or their establishment and persistence in these isolated and hostile regions.
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Affiliation(s)
- Álvaro Del Moral
- Department of Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences (MNCN), CSIC, Serrano 115 dpdo, E-28006 Madrid, Spain.,AstrobiologyOU, School of Environment, Earth and Ecosystem Sciences, STEM Faculty, The Open University, Walton Hall, Kents Hill, MK7 6AA, Milton Keynes, UK
| | - Isaac Garrido-Benavent
- Department of Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences (MNCN), CSIC, Serrano 115 dpdo, E-28006 Madrid, Spain
| | - Jorge Durán
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calzada Martin de Freitas, 3000-456 Coimbra, Portugal
| | - Jan R Lehmann
- Remote Sensing and Spatial Modelling, Institute of Landscape Ecology, University of Münster, Heisenbergstrasse 2, 48149 Münster, Germany
| | - Alexandra Rodríguez
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calzada Martin de Freitas, 3000-456 Coimbra, Portugal
| | - Starri Heiðmarsson
- Icelandic Institute of Natural History, Borgir vio Noroursloo 600-Akureyri, Iceland
| | - Asunción de Los Ríos
- Department of Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences (MNCN), CSIC, Serrano 115 dpdo, E-28006 Madrid, Spain
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24
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Bioactive Secondary Metabolites from Psychrophilic Fungi and Their Industrial Importance. Fungal Biol 2021. [DOI: 10.1007/978-3-030-85603-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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25
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Applications of red pigments from psychrophilic Rhodonellum psychrophilum GL8 in health, food and antimicrobial finishes on textiles. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.03.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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26
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Xia JM, Hu XM, Huang CH, Yu LB, Xu RF, Tang XX, Lin DH. Metabolic profiling of cold adaptation of a deep-sea psychrotolerant Microbacterium sediminis to prolonged low temperature under high hydrostatic pressure. Appl Microbiol Biotechnol 2019; 104:277-289. [PMID: 31728583 DOI: 10.1007/s00253-019-10134-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/30/2019] [Accepted: 09/08/2019] [Indexed: 12/01/2022]
Abstract
The most wide-spread "hostile" environmental factor for marine microorganisms is low temperature, which is usually accompanied by high hydrostatic pressure (HHP). Metabolic mechanisms of marine microorganisms adapting to prolonged low temperature under HHP remain to be clarified. To reveal the underlying metabolic mechanisms, we performed NMR-based metabolomic analysis of aqueous extracts derived from a psychrotolerant Microbacterium sediminis YLB-01, which was isolated from deep-sea sediment and possess great biotechnology potentials. The YLB-01 cells were firstly cultivated at the optimal condition (28 °C, 0.1 MPa) for either 18 h (logarithmic phase) or 24 h (stationary phase), then continually cultivated at either 28 °C or 4 °C under HHP (30 MPa) for 7 days. The cells cultivated at low temperature, which experienced cold stress, were distinctly distinguished from those at normal temperature. Cold stress primarily induced metabolic changes in amino acid metabolism and carbohydrate metabolism. Furthermore, the logarithmic and stationary phase cells cultivated at low temperature exhibited distinct metabolic discrimination, which was mostly reflected in the significantly disturbed carbohydrate metabolism. The logarithmic phase cells displayed suppressed TCA cycle, while the stationary phase cells showed decreased pyruvate and increased lactate. In addition, we performed transcriptome analysis for the stationary phase cells to support the metabolomic analysis. Our results suggest that the cold adaptation of the psychrotroph YLB-01 is closely associated with profoundly altered amino acid metabolism and carbohydrate metabolism. Our work provides a mechanistic understanding of the metabolic adaptation of marine psychrotrophs to prolonged low temperature under HHP.
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Affiliation(s)
- Jin-Mei Xia
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Xiamen, 361005, China
| | - Xiao-Min Hu
- College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Xiamen University, Xiamen, 361005, China
| | - Cai-Hua Huang
- Research and Communication Center of Exercise and Health, Xiamen University of Technology, Xiamen, 361024, China
| | - Li-Bo Yu
- China Ocean Sample Respository (Biology), 184 Daxue Road, Xiamen, 361005, China
| | - Ru-Fang Xu
- China Ocean Sample Respository (Biology), 184 Daxue Road, Xiamen, 361005, China
| | - Xi-Xiang Tang
- China Ocean Sample Respository (Biology), 184 Daxue Road, Xiamen, 361005, China.
| | - Dong-Hai Lin
- College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Xiamen University, Xiamen, 361005, China.
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27
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Kumar V, Kumar S, Singh D. Microbial polyhydroxyalkanoates from extreme niches: Bioprospection status, opportunities and challenges. Int J Biol Macromol 2019; 147:1255-1267. [PMID: 31739043 DOI: 10.1016/j.ijbiomac.2019.09.253] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 09/23/2019] [Accepted: 09/30/2019] [Indexed: 01/20/2023]
Abstract
Extreme niches are offered with unusual physiochemical conditions that impose stress to the life-forms including microbial communities. Microbes have evolved unique physiology and genetics to interact dynamically with extreme environments for their adaptation and survival. Amongst the several adaptive features of microbes in stressed conditions, polyhydroxyalkanoates synthesis is a crucial strategy of many bacteria and archaea to reserve carbon and energy inside the cell. Apart from the relevance of PHA to microbial world, these intracellular polyesters are seen as essential biological macromolecules for the bio-material industry owing to their plastic-like properties, biodegradable and eco-friendly nature. Recently, much attention has been attracted by the microbes of extreme habitats for a new source of industrially suited PHA producers and novel PHA with unique properties. Therefore, the current review is focused on the critical evaluation of microbes from extreme niches for PHA production and opportunities for the development of commercially feasible PHA bioprocess.
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Affiliation(s)
- Vijay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176 061, India
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176 061, India
| | - Dharam Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176 061, India.
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28
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Bazhenov SV, Khrulnova SA, Konopleva MN, Manukhov IV. Seasonal changes in luminescent intestinal microflora of the fish inhabiting the Bering and Okhotsk seas. FEMS Microbiol Lett 2019; 366:5322163. [PMID: 30772893 DOI: 10.1093/femsle/fnz040] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 02/15/2019] [Indexed: 11/14/2022] Open
Abstract
Here, we present a study of luminescent intestinal microflora of the fish inhabiting Bering and Okhotsk seas in summer and winter seasons. Sampling of intestinal luminescent microflora was carried for several years, with all recovered species belonging to psychrophilic bacteria of either Aliivibrio logei or Photobacterium phosphoreum species. A seasonal change in fish intestinal luminescent microflora detected include an increase in prevalence of P. phosphoreum bacteria in summer and an increase in prevalence of A. logei bacteria in winter seasons. In fact, 90% of all luminescent bacteria isolated in winter period (January-March) were A. logei, while 88% of luminescent isolates recovered in summer period (July-September) were that of P. phosphoreum species. Seasonal changes were similar across all six sampling expeditions, three in winter and three in summer seasons, evenly spread through 2010-2018 period.
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Affiliation(s)
- Sergey V Bazhenov
- Laboratory of Molecular Genetics, Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation.,State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center "Kurchatov Institute", 1st Dorozhnii pr., 1, Moscow 117545, Russian Federation
| | - Svetlana A Khrulnova
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center "Kurchatov Institute", 1st Dorozhnii pr., 1, Moscow 117545, Russian Federation
| | - Maria N Konopleva
- Laboratory of Molecular Genetics, Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation
| | - Ilya V Manukhov
- Laboratory of Molecular Genetics, Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation.,State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center "Kurchatov Institute", 1st Dorozhnii pr., 1, Moscow 117545, Russian Federation
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29
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Papale M, Lo Giudice A, Conte A, Rizzo C, Rappazzo AC, Maimone G, Caruso G, La Ferla R, Azzaro M, Gugliandolo C, Paranhos R, Cabral AS, Romano Spica V, Guglielmin M. Microbial Assemblages in Pressurized Antarctic Brine Pockets (Tarn Flat, Northern Victoria Land): A Hotspot of Biodiversity and Activity. Microorganisms 2019; 7:E333. [PMID: 31505750 PMCID: PMC6780602 DOI: 10.3390/microorganisms7090333] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 12/03/2022] Open
Abstract
Two distinct pressurized hypersaline brine pockets (named TF4 and TF5), separated by a thin ice layer, were detected below an ice-sealed Antarctic lake. Prokaryotic (bacterial and archaeal) diversity, abundances (including virus-like particles) and metabolic profiles were investigated by an integrated approach, including traditional and new-generation methods. Although similar diversity indices were computed for both Bacteria and Archaea, distinct bacterial and archaeal assemblages were observed. Bacteroidetes and Gammaproteobacteria were more abundant in the shallowest brine pocket, TF4, and Deltaproteobacteria, mainly represented by versatile sulphate-reducing bacteria, dominated in the deepest, TF5. The detection of sulphate-reducing bacteria and methanogenic Archaea likely reflects the presence of a distinct synthrophic consortium in TF5. Surprisingly, members assigned to hyperthermophilic Crenarchaeota and Euryarchaeota were common to both brines, indicating that these cold habitats host the most thermally tolerant Archaea. The patterns of microbial communities were different, coherently with the observed microbiological diversity between TF4 and TF5 brines. Both the influence exerted by upward movement of saline brines from a sub-surface anoxic system and the possible occurrence of an ancient ice remnant from the Ross Ice Shelf were the likely main factors shaping the microbial communities.
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Affiliation(s)
- Maria Papale
- Institute of Polar Sciences, National Research Council (ISP-CNR), 98122 Messina, Italy.
| | - Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council (ISP-CNR), 98122 Messina, Italy.
| | - Antonella Conte
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98168 Messina, Italy.
| | - Carmen Rizzo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98168 Messina, Italy.
| | - Alessandro C Rappazzo
- Institute of Polar Sciences, National Research Council (ISP-CNR), 98122 Messina, Italy.
| | - Giovanna Maimone
- Institute of Polar Sciences, National Research Council (ISP-CNR), 98122 Messina, Italy.
| | - Gabriella Caruso
- Institute of Polar Sciences, National Research Council (ISP-CNR), 98122 Messina, Italy.
| | - Rosabruna La Ferla
- Institute of Polar Sciences, National Research Council (ISP-CNR), 98122 Messina, Italy.
| | - Maurizio Azzaro
- Institute of Polar Sciences, National Research Council (ISP-CNR), 98122 Messina, Italy.
| | - Concetta Gugliandolo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98168 Messina, Italy.
| | - Rodolfo Paranhos
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro 21.941-590, Brazil.
| | - Anderson S Cabral
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro 21.941-590, Brazil.
| | - Vincenzo Romano Spica
- Department of Movement, Human and Health Sciences, Public Health Unit, University of Rome "Foro Italico", P.zza Lauro De Bosis 6, 00135 Rome, Italy.
| | - Mauro Guglielmin
- Dipartimento di Scienze Teoriche e Applicate, University of Insubria, 21100 Varese, Italy.
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30
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Taxonomic and functional characterization of a microbial community from a volcanic englacial ecosystem in Deception Island, Antarctica. Sci Rep 2019; 9:12158. [PMID: 31434915 PMCID: PMC6704131 DOI: 10.1038/s41598-019-47994-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/24/2019] [Indexed: 12/22/2022] Open
Abstract
Glaciers are populated by a large number of microorganisms including bacteria, archaea and microeukaryotes. Several factors such as solar radiation, nutrient availability and water content greatly determine the diversity and abundance of these microbial populations, the type of metabolism and the biogeochemical cycles. Three ecosystems can be differentiated in glaciers: supraglacial, subglacial and englacial ecosystems. Firstly, the supraglacial ecosystem, sunlit and oxygenated, is predominantly populated by photoautotrophic microorganisms. Secondly, the subglacial ecosystem contains a majority of chemoautotrophs that are fed on the mineral salts of the rocks and basal soil. Lastly, the englacial ecosystem is the least studied and the one that contains the smallest number of microorganisms. However, these unknown englacial microorganisms establish a food web and appear to have an active metabolism. In order to study their metabolic potentials, samples of englacial ice were taken from an Antarctic glacier. Microorganisms were analyzed by a polyphasic approach that combines a set of -omic techniques: 16S rRNA sequencing, culturomics and metaproteomics. This combination provides key information about diversity and functions of microbial populations, especially in rare habitats. Several whole essential proteins and enzymes related to metabolism and energy production, recombination and translation were found that demonstrate the existence of cellular activity at subzero temperatures. In this way it is shown that the englacial microorganisms are not quiescent, but that they maintain an active metabolism and play an important role in the glacial microbial community.
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31
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Kim J, Chang W. Modified soil respiration model (URESP) extended to sub-zero temperatures for biostimulated petroleum hydrocarbon-contaminated sub-Arctic soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 667:400-411. [PMID: 30831374 DOI: 10.1016/j.scitotenv.2019.02.067] [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: 10/31/2018] [Revised: 01/28/2019] [Accepted: 02/04/2019] [Indexed: 06/09/2023]
Abstract
It has been increasingly reported that aerobic soil respiration activity (CO2 production and O2 consumption) is measurable in frozen cold-climate soils. This study modifies the Generalized Respiration (GRESP) model, a function of soil temperature (T) and unfrozen water content (M), to cover the frozen, partially frozen and unfrozen phases of successfully bioremediated, petroleum hydrocarbon-contaminated, sandy sub-Arctic soils. The Michaelis-Menten equation was modified to express the observable change in unfrozen water content near 0 °C, which is related to soil respiration activity during soil phase changes and at temperatures below the effective endpoint of detectable unfrozen water at -2 °C. The modified Michaelis-Menten equation was further combined with a Q10 temperature term, and was then incorporated into the GRESP equation to produce a new URESP model for the engineered soil bioremediation system at sub-zero temperatures. The URESP model was applied to published input data measured from the biostimulated site soils of a pilot-scale soil tank experiment conducted between -5 and 15 °C. The model fit well with the experimental data for CO2 production (R2 = 0.96) and O2 consumption (R2 = 0.92). A numerical soil thermal model (TEMP/W model) of the thawing biotreated soils in the tank was also used in this study to produce valid alternative (predictive) input T and M data for the URESP model. The URESP-derived respiration quotients (RQ; 0.695 to 0.698), or the ratios of CO2 production to O2 consumption, aligned with the experimental RQ values from the soil tank experiment (0.69) and fell within the theoretical RQ range for aerobic hydrocarbon degradation (0.63-0.80). The URESP model combined with the TEMP/W simulation approximated changes in soil respiration during thawing and characterized the computed soil respiration outputs as related to hydrocarbon utilization, based on their RQ values.
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Affiliation(s)
- Jihun Kim
- Department of Civil, Geological and Environmental Engineering, University of Saskatchewan, Canada
| | - Wonjae Chang
- Department of Civil, Geological and Environmental Engineering, University of Saskatchewan, Canada.
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32
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Paun VI, Icaza G, Lavin P, Marin C, Tudorache A, Perşoiu A, Dorador C, Purcarea C. Total and Potentially Active Bacterial Communities Entrapped in a Late Glacial Through Holocene Ice Core From Scarisoara Ice Cave, Romania. Front Microbiol 2019; 10:1193. [PMID: 31244788 PMCID: PMC6563852 DOI: 10.3389/fmicb.2019.01193] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 05/13/2019] [Indexed: 01/20/2023] Open
Abstract
Our understanding of the icy-habitat microbiome is likely limited by a lack of reliable data on microorganisms inhabiting underground ice that has accumulated inside caves. To characterize how environmental variation impacts cave ice microbial community structure, we determined the composition of total and potentially active bacterial communities along a 13,000-year-old ice core from Scarisoara cave (Romania) through 16S rRNA gene Illumina sequencing. An average of 2,546 prokaryotic gDNA operational taxonomic units (OTUs) and 585 cDNA OTUs were identified across the perennial cave ice block and analyzed in relation to the geochemical composition of ice layers. The total microbial community and the putative active fraction displayed dissimilar taxa profiles. The ice-contained microbiome was dominated by Actinobacteria with a variable representation of Proteobacteria, while the putative active microbial community was equally shared between Proteobacteria and Firmicutes. Accordingly, a major presence of Cryobacterium, Lysinomonas, Pedobacter, and Aeromicrobium phylotypes homologous to psychrotrophic and psychrophilic bacteria from various cold environments were noted in the total community, while the prevalent putative active bacteria belonged to Clostridium, Pseudomonas, Janthinobacterium, Stenotrophomonas, and Massilia genera. Variation in the microbial cell density of ice strata with the dissolved organic carbon (DOC) content and the strong correlation of DOC and silicon concentrations revealed a major impact of depositional processes on microbial abundance throughout the ice block. Post-depositional processes appeared to occur mostly during the 4,000–7,000 years BP interval. A major bacterial composition shift was observed in 4,500–5,000-year-old ice, leading to a high representation of Beta- and Deltaproteobacteria in the potentially active community in response to the increased concentrations of DOC and major chemical elements. Estimated metabolic rates suggested the presence of a viable microbial community within the cave ice block, characterized by a maintenance metabolism in most strata and growth capacity in those ice deposits with high microbial abundance and DOC content. This first survey of microbial distribution in perennial cave ice formed since the Last Glacial period revealed a complex potentially active community, highlighting major shifts in community composition associated with geochemical changes that took place during climatic events that occurred about 5,000 years ago, with putative formation of photosynthetic biofilms.
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Affiliation(s)
- Victoria I Paun
- Department of Microbiology, Institute of Biology, Bucharest, Romania
| | - Gonzalo Icaza
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Antofagasta, Chile
| | - Paris Lavin
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile.,Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Constantin Marin
- Laboratory of Hydrogeochemistry, "Emil Racovita" Institute of Speleology, Bucharest, Romania
| | - Alin Tudorache
- Laboratory of Hydrogeochemistry, "Emil Racovita" Institute of Speleology, Bucharest, Romania
| | - Aurel Perşoiu
- Department of Microbiology, Institute of Biology, Bucharest, Romania.,"Emil Racovita" Institute of Speleology, Cluj-Napoca, Romania.,Stefan cel Mare University of Suceava, Suceava, Romania
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Antofagasta, Chile.,Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Cristina Purcarea
- Department of Microbiology, Institute of Biology, Bucharest, Romania
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33
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Singh D, Thakur S, Thayil SM, Kesavan AK. Characterization of a cold-active, detergent-stable metallopeptidase purified from Bacillus sp. S1DI 10 using Response Surface Methodology. PLoS One 2019; 14:e0216990. [PMID: 31120932 PMCID: PMC6532869 DOI: 10.1371/journal.pone.0216990] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 05/02/2019] [Indexed: 01/23/2023] Open
Abstract
The colder regions of Earth are inhabited by cold-adapted microorganisms designated as psychrophiles that are known to produce cold-active enzymes, such as peptidases, chaperones, lipases, cellulases, and phosphatases. These types of enzymes are a major part of the market of industrial enzymes. Bacteria isolated from water samples collected from the Chamba region in the Himalayas were screened for peptidase production using skim milk agar plates. Among the peptidase-producing bacteria isolated, 20% of the isolates exhibited fast growth and maximum zones of clearance, and thus, were used for further studies. The 16S rDNA sequence analysis of isolate S1DI 10 identified it as a Bacillus sp. The peptidase was cloned in pET28a vector and expressed in Escherichia coli BL21(DE3) and the His-tagged recombinant protein was purified using Ni-NTA column. The purified peptidase of SIDI 10 was found to be an alkaline, cold-active peptidase with optimal enzyme activity at 10°C and pH 8. An approach of one variable at a time was used to further study the effect of various metal ions, organic solvents and detergents on the peptidase enzyme. The peptidase activity was enhanced in the presence of Fe2+ and Mn2+ (metal ions), hexane (organic solvent), SDS- sodium dodecyl sulfate (anionic detergent) and Tween 80 (nonionic detergent). Response surface methodology (RSM) was used to determine the cumulative effect of these five variables. A 25 full factorial central composite design was applied for the five independent variables to determine the optimal combinations of these constituents at the maximum peptidase activity.
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Affiliation(s)
- Drishtant Singh
- Molecular Microbiology Lab, Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Sharad Thakur
- Molecular Microbiology Lab, Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Seema Madhumal Thayil
- Molecular Microbiology Lab, Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Anup Kumar Kesavan
- Molecular Microbiology Lab, Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, India
- * E-mail:
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34
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Wong CMVL, Boo SY, Voo CLY, Zainuddin N, Najimudin N. A comparative transcriptomic analysis provides insights into the cold-adaptation mechanisms of a psychrophilic yeast, Glaciozyma antarctica PI12. Polar Biol 2019. [DOI: 10.1007/s00300-018-02443-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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Laganà P, Caruso G, Corsi I, Bergami E, Venuti V, Majolino D, La Ferla R, Azzaro M, Cappello S. Do plastics serve as a possible vector for the spread of antibiotic resistance? First insights from bacteria associated to a polystyrene piece from King George Island (Antarctica). Int J Hyg Environ Health 2019; 222:89-100. [DOI: 10.1016/j.ijheh.2018.08.009] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/14/2018] [Accepted: 08/15/2018] [Indexed: 11/25/2022]
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36
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Cold survival strategies for bacteria, recent advancement and potential industrial applications. Arch Microbiol 2018; 201:1-16. [PMID: 30478730 DOI: 10.1007/s00203-018-1602-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/04/2018] [Accepted: 11/24/2018] [Indexed: 12/12/2022]
Abstract
Microorganisms have evolved themselves to thrive under various extreme environmental conditions such as extremely high or low temperature, alkalinity, and salinity. These microorganisms adapted several metabolic processes to survive and reproduce efficiently under such extreme environments. As the major proportion of earth is covered with the cold environment and is exploited by human beings, these sites are not pristine anymore. Human interventions are a great reason for disturbing the natural biogeochemical cycles in these regions. The survival strategies of these organisms have shown great potential for helping us to restore these pristine sites and the use of isolated cold-adapted enzymes from these organisms has also revolutionized various industrial products. This review gives you the insight of psychrophilic enzyme adaptations and their industrial applications.
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37
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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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38
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Zhang X, Li SJ, Li JJ, Liang ZZ, Zhao CQ. Novel Natural Products from Extremophilic Fungi. Mar Drugs 2018; 16:md16060194. [PMID: 29867059 PMCID: PMC6025453 DOI: 10.3390/md16060194] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 05/31/2018] [Accepted: 06/02/2018] [Indexed: 12/19/2022] Open
Abstract
Extremophilic fungi have been found to develop unique defences to survive extremes of pressure, temperature, salinity, desiccation, and pH, leading to the biosynthesis of novel natural products with diverse biological activities. The present review focuses on new extremophilic fungal natural products published from 2005 to 2017, highlighting the chemical structures and their biological potential.
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Affiliation(s)
- Xuan Zhang
- Gene Engineering and Biotechnology Beijing Key Laboratory, Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China.
| | - Shou-Jie Li
- Gene Engineering and Biotechnology Beijing Key Laboratory, Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China.
| | - Jin-Jie Li
- Gene Engineering and Biotechnology Beijing Key Laboratory, Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China.
| | - Zi-Zhen Liang
- Gene Engineering and Biotechnology Beijing Key Laboratory, Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China.
| | - Chang-Qi Zhao
- Gene Engineering and Biotechnology Beijing Key Laboratory, Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China.
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39
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Liu D, Huang Y, Yan H, Jiang Y, Zhao T, An S. Dynamics of soil nitrogen fractions and their relationship with soil microbial communities in two forest species of northern China. PLoS One 2018; 13:e0196567. [PMID: 29795562 PMCID: PMC5967799 DOI: 10.1371/journal.pone.0196567] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 04/16/2018] [Indexed: 11/19/2022] Open
Abstract
Microbially-mediated soil N mineralization and transformation are crucial to plant growth. However, changes in soil microbial groups and various N components are not clearly understood. To explore the relationship between soil N components and microbial communities, we conducted an in-situ experiment on two typically planted forest species, namely, Sibirica Apricot (SA) and Prunus davidiana Franch (PdF) by using closed-top polyvinyl chloride tubes. Changes in soil inorganic N, organic N (ON) fractions, and levels of microbial phospholipid fatty acids (PLFAs) were measured bimonthly from April 2012 to April 2013. Microbial PLFAs and the concentrations of easily-available microbial biomass N (MBN; ~60 mg kg-1), soluble ON (SON; ~20 mg kg-1), and inorganic N were similar between the two soils whereas the ON (~900 mg kg-1) and its major part total acid-hydrolyzable N (HTN; ~500 mg kg-1), were significantly different (p < 0.05) in most months (5/6 and 4/6; respectively). The canonical correlation analysis of soil N fractions and microbial parameters indicated that the relationship between total PLFAs (total biomass of living cells) and NH4+-N was the most representative. The relative contributions (indicated by the absolute value of canonical coefficient) of NH4+-N were the largest, followed by NO3--N and MBN. For the HTN component, the relative percentage of hydrolyzable amino acid N and ammonium N decreased markedly in the first half of the year. Canonical variation mainly reflected the relationship between ammonium N and bacterial PLFAs, which were the most sensitive indicators related to soil N changes. The relative contributions of HTN components to the link between soil microbial groups and HTN components were ammonium N > amino acid N > amino sugar N. Observations from our study indicate the sensitivity of soil N mineralization indicators in relation to the temporal variation of soil microbial groups and N fractions.
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Affiliation(s)
- Dong Liu
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, College of Resource and Environment Science, Northwest A&F University, Yangling, China
- State Key Laboratory of Soil Erosion and Dryland Farming on Loess Plateau, Northwest A&F University, Yangling, China
| | - Yimei Huang
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, College of Resource and Environment Science, Northwest A&F University, Yangling, China
- * E-mail:
| | - Hao Yan
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, College of Resource and Environment Science, Northwest A&F University, Yangling, China
| | - Yueli Jiang
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, College of Resource and Environment Science, Northwest A&F University, Yangling, China
| | - Tong Zhao
- Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, College of Resource and Environment Science, Northwest A&F University, Yangling, China
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dryland Farming on Loess Plateau, Northwest A&F University, Yangling, China
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40
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Bacteria from Antarctic environments: diversity and detection of antimicrobial, antiproliferative, and antiparasitic activities. Polar Biol 2018. [DOI: 10.1007/s00300-018-2300-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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41
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Psychrotrophic Microbiomes: Molecular Diversity and Beneficial Role in Plant Growth Promotion and Soil Health. MICROORGANISMS FOR SUSTAINABILITY 2018. [DOI: 10.1007/978-981-10-7146-1_11] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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42
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Nievola CC, Carvalho CP, Carvalho V, Rodrigues E. Rapid responses of plants to temperature changes. Temperature (Austin) 2017; 4:371-405. [PMID: 29435478 PMCID: PMC5800372 DOI: 10.1080/23328940.2017.1377812] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 12/15/2022] Open
Abstract
Temperature is one of the main environmental factors that affect plant metabolism. Considering that plants are sessile, their survival depends on the efficient activation of resistance responses to thermal stress. In this comprehensive review, we discuss recent work on rapid biochemical and physiological adjustments, herein referred to as those occurring during the first few hours or a few days after the beginning of the change in the ambient temperature. The short-term metabolic modulation after plant exposure to heat and cold, including chilling and freezing, is discussed. Effects on photosynthesis, cell membranes, antioxidant system, production of heat shock proteins and nitric oxide, as well as an overview of signaling events to heat or cold stress are presented. In addition, we also discuss the acclimation process that occurs when the plant acquires resistance to an increase or decrease in temperature, adjusting its homeostasis and steady-state physiology to the new temperatures. Finally, we present studies with tropical plants that aim at elucidating the effects of temperature and the identification of the resilience levels of these plants to the expected climate changes, and which seek the development of techniques for germplasm conservation of endangered species.
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Affiliation(s)
- Catarina C. Nievola
- Núcleo de Pesquisa em Plantas Ornamentais, Instituto de Botânica SMA/SP, São Paulo, SP, Brazil
| | - Camila P. Carvalho
- Núcleo de Pesquisa em Plantas Ornamentais, Instituto de Botânica SMA/SP, São Paulo, SP, Brazil
| | - Victória Carvalho
- Núcleo de Pesquisa em Plantas Ornamentais, Instituto de Botânica SMA/SP, São Paulo, SP, Brazil
| | - Edson Rodrigues
- Instituto Básico de Biociências, Universidade de Taubaté, Taubaté, SP, Brazil
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43
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Feller G. Protein folding at extreme temperatures: Current issues. Semin Cell Dev Biol 2017; 84:129-137. [PMID: 28941878 DOI: 10.1016/j.semcdb.2017.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 08/18/2017] [Accepted: 09/05/2017] [Indexed: 10/18/2022]
Abstract
The range of temperatures compatible with life is currently estimated from -25°C, as exemplified by metabolically active bacteria between sea ice crystals, and up to 122°C in hydrothermal vents as exemplified by the archaeon Methanopyrus kandleri. In the context of protein folding, as soon as a polypeptide emerges from the ribosome, it is exposed to the effects of environmental temperatures. Recent investigations have shown that the rate of protein folding is not adapted to extreme temperatures and should be very fast at high temperature and low in cold environments. This lack of adaptation is driven by kinetic constraints on protein stability. To counteract the deleterious effects of fast protein folding in hyperthermophiles, chaperones such as the Trigger Factor hold and slow down the rate of folding intermediates. Prolyl isomerization, a rate-limiting step in the folding of many proteins, is strongly temperature-dependent and impairs folding of psychrophilic proteins in the cold. This is compensated by reduction of the proline content in cold-adapted proteins, by an increased number of prolyl isomerases encoded in the genome of psychrophilic microorganisms and by overexpression of prolyl isomerases under low temperature cultivation. After folding, the native state is reached and although extremophilic proteins share the same fold, dramatic differences in stability have been recorded by differential scanning calorimetry.
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Affiliation(s)
- Georges Feller
- Laboratory of Biochemistry, Center for Protein Engineering-InBioS, University of Liège, Institute of Chemistry B6a, 4000 Liège-Sart Tilman, Belgium.
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La Ferla R, Azzaro M, Michaud L, Caruso G, Lo Giudice A, Paranhos R, Cabral AS, Conte A, Cosenza A, Maimone G, Papale M, Rappazzo AC, Guglielmin M. Prokaryotic Abundance and Activity in Permafrost of the Northern Victoria Land and Upper Victoria Valley (Antarctica). MICROBIAL ECOLOGY 2017; 74:402-415. [PMID: 28289836 DOI: 10.1007/s00248-017-0955-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 02/20/2017] [Indexed: 06/06/2023]
Abstract
Victoria Land permafrost harbours a potentially large pool of cold-affected microorganisms whose metabolic potential still remains underestimated. Three cores (BC-1, BC-2 and BC-3) drilled at different depths in Boulder Clay (Northern Victoria Land) and one sample (DY) collected from a core in the Dry Valleys (Upper Victoria Valley) were analysed to assess the prokaryotic abundance, viability, physiological profiles and potential metabolic rates. The cores drilled at Boulder Clay were a template of different ecological conditions (different temperature regime, ice content, exchanges with atmosphere and with liquid water) in the same small basin while the Dry Valleys site was very similar to BC-2 conditions but with a complete different geological history and ground ice type. Image analysis was adopted to determine cell abundance, size and shape as well as to quantify the potential viable and respiring cells by live/dead and 5-cyano-2,3-ditolyl-tetrazolium chloride staining, respectively. Subpopulation recognition by apparent nucleic acid contents was obtained by flow cytometry. Moreover, the physiological profiles at community level by Biolog-Ecoplate™ as well as the ectoenzymatic potential rates on proteinaceous (leucine-aminopeptidase) and glucidic (ß-glucosidase) organic matter and on organic phosphates (alkaline-phosphatase) by fluorogenic substrates were tested. The adopted methodological approach gave useful information regarding viability and metabolic performances of microbial community in permafrost. The occurrence of a multifaceted prokaryotic community in the Victoria Land permafrost and a large number of potentially viable and respiring cells (in the order of 104-105) were recognised. Subpopulations with a different apparent DNA content within the different samples were observed. The physiological profiles stressed various potential metabolic pathways among the samples and intense utilisation rates of polymeric carbon compounds and carbohydrates, mainly in deep samples. The measured enzymatic activity rates suggested the potential capability of the microbial community to decompose proteins and polysaccharides. The microbial community seems to be appropriate to contribute to biogeochemical cycling in this extreme environment.
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Affiliation(s)
- Rosabruna La Ferla
- National Council of Research (IAMC-CNR), Institute for Coastal Marine Environment, Spianata San Raineri 86, 98122, Messina, Italy.
| | - Maurizio Azzaro
- National Council of Research (IAMC-CNR), Institute for Coastal Marine Environment, Spianata San Raineri 86, 98122, Messina, Italy
| | - Luigi Michaud
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Gabriella Caruso
- National Council of Research (IAMC-CNR), Institute for Coastal Marine Environment, Spianata San Raineri 86, 98122, Messina, Italy
| | - Angelina Lo Giudice
- National Council of Research (IAMC-CNR), Institute for Coastal Marine Environment, Spianata San Raineri 86, 98122, Messina, Italy
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Rodolfo Paranhos
- Institute of Biology, Federal University of Rio de Janeiro, Prédio do CCS, Cidade Universitária do Fundao, Rio de Janeiro, Brazil
| | - Anderson S Cabral
- Institute of Biology, Federal University of Rio de Janeiro, Prédio do CCS, Cidade Universitária do Fundao, Rio de Janeiro, Brazil
| | - Antonella Conte
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Alessandro Cosenza
- National Council of Research (IAMC-CNR), Institute for Coastal Marine Environment, Spianata San Raineri 86, 98122, Messina, Italy
| | - Giovanna Maimone
- National Council of Research (IAMC-CNR), Institute for Coastal Marine Environment, Spianata San Raineri 86, 98122, Messina, Italy
| | - Maria Papale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Alessandro Ciro Rappazzo
- National Council of Research (IAMC-CNR), Institute for Coastal Marine Environment, Spianata San Raineri 86, 98122, Messina, Italy
| | - Mauro Guglielmin
- Department of Theoretical and Applied Sciences, University of Insubria, Via J.H. Dunant 3, Varese, Italy
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45
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Casillo A, Ziaco M, Lindner B, Parrilli E, Schwudke D, Holgado A, Verstrepen L, Sannino F, Beyaert R, Lanzetta R, Tutino ML, Corsaro MM. Unusual Lipid A from a Cold-Adapted Bacterium: Detailed Structural Characterization. Chembiochem 2017. [PMID: 28650563 DOI: 10.1002/cbic.201700287] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Colwellia psychrerythraea 34H is a Gram-negative cold-adapted microorganism that adopts many strategies to cope with the limitations associated with the low temperatures of its habitat. In this study, we report the complete characterization of the lipid A moiety from the lipopolysaccharide of Colwellia. Lipid A and its partially deacylated derivative were completely characterized by high-resolution mass spectrometry, NMR spectroscopy, and chemical analysis. An unusual structure with a 3-hydroxy unsaturated tetradecenoic acid as a component of the primary acylation pattern was identified. In addition, the presence of a partially acylated phosphoglycerol moiety on the secondary acylation site at the 3-position of the reducing 2-amino-2-deoxyglucopyranose unit caused tremendous natural heterogeneity in the structure of lipid A. Biological-activity assays indicated that C. psychrerythraea 34H lipid A did not show an agonistic or antagonistic effect upon testing in human macrophages.
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Affiliation(s)
- Angela Casillo
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126, Naples, Italy
| | - Marcello Ziaco
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126, Naples, Italy
| | - Buko Lindner
- Division of Bioanalytical Chemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 10, 23845, Borstel, Germany
| | - Ermenegilda Parrilli
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126, Naples, Italy
| | - Dominik Schwudke
- Division of Bioanalytical Chemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 10, 23845, Borstel, Germany
| | - Aurora Holgado
- Unit for Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, VIB, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium
| | - Lynn Verstrepen
- Unit for Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, VIB, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium
| | - Filomena Sannino
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126, Naples, Italy
| | - Rudi Beyaert
- Unit for Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, VIB, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium
| | - Rosa Lanzetta
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126, Naples, Italy
| | - Maria Luisa Tutino
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126, Naples, Italy
| | - Maria Michela Corsaro
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126, Naples, Italy
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46
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Cryosphere and Psychrophiles: Insights into a Cold Origin of Life? Life (Basel) 2017; 7:life7020025. [PMID: 28604605 PMCID: PMC5492147 DOI: 10.3390/life7020025] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/06/2017] [Accepted: 06/08/2017] [Indexed: 11/23/2022] Open
Abstract
Psychrophiles thrive permanently in the various cold environments on Earth. Their unsuspected ability to remain metabolically active in the most extreme low temperature conditions provides insights into a possible cold step in the origin of life. More specifically, metabolically active psychrophilic bacteria have been observed at −20 °C in the ice eutectic phase (i.e., the liquid veins between sea ice crystals). In the context of the RNA world hypothesis, this ice eutectic phase would have provided stability to the RNA molecules and confinement of the molecules in order to react and replicate. This aspect has been convincingly tested by laboratory experiments.
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47
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Microbial Diversity in Extreme Marine Habitats and Their Biomolecules. Microorganisms 2017; 5:microorganisms5020025. [PMID: 28509857 PMCID: PMC5488096 DOI: 10.3390/microorganisms5020025] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/02/2017] [Accepted: 05/11/2017] [Indexed: 11/17/2022] Open
Abstract
Extreme marine environments have been the subject of many studies and scientific publications. For many years, these environmental niches, which are characterized by high or low temperatures, high-pressure, low pH, high salt concentrations and also two or more extreme parameters in combination, have been thought to be incompatible to any life forms. Thanks to new technologies such as metagenomics, it is now possible to detect life in most extreme environments. Starting from the discovery of deep sea hydrothermal vents up to the study of marine biodiversity, new microorganisms have been identified, and their potential uses in several applied fields have been outlined. Thermophile, halophile, alkalophile, psychrophile, piezophile and polyextremophile microorganisms have been isolated from these marine environments; they proliferate thanks to adaptation strategies involving diverse cellular metabolic mechanisms. Therefore, a vast number of new biomolecules such as enzymes, polymers and osmolytes from the inhabitant microbial community of the sea have been studied, and there is a growing interest in the potential returns of several industrial production processes concerning the pharmaceutical, medical, environmental and food fields.
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48
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Karppinen EM, Stewart KJ, Farrell RE, Siciliano SD. Petroleum hydrocarbon remediation in frozen soil using a meat and bonemeal biochar plus fertilizer. CHEMOSPHERE 2017; 173:330-339. [PMID: 28122292 DOI: 10.1016/j.chemosphere.2017.01.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/09/2016] [Accepted: 01/03/2017] [Indexed: 06/06/2023]
Abstract
Petroleum hydrocarbon (PHC) degradation slows significantly during the winter which substantially increases the time it takes to remediate soil in Arctic landfarms. The aim of this laboratory trial was to assess the potential of a meat and bonemeal (MBM) biochar to stimulate PHC degradation in contaminated soil collected from Iqaluit, Canada. Over 90 days, 3% (w/w) MBM biochar significantly increased F3- (equivalent nC16-C34) PHC degradation rate constants (k) in frozen soils when compared to the fertilizer (urea and monoammonium phosphate) control. Taking into consideration extensive variability within treatments and negative k values, this difference may not reflect significant remediation. Decreasing C17/Pr and C18/Ph ratios in the frozen soil suggest that this reduction is a result of microbial degradation rather than volatilization. Amendment type and application rate affected the immediate abiotic losses of F2 and F3-PHC in sterile soils, with the greatest losses occurring in compost-amended treatments in the first 24 h. In frozen soils, MBM biochar was found to increase liquid water content (θliquid) but not nutrient supply rates. Under frozen but not thawed conditions, genes for aromatic (C2,3O and nahAc) but not aliphatic (alkB) PHC degradation increased over time in both biochar-amended and control treatments but total viable PHC-degrading populations only increased in biochar-amended soils. Based on these results, it is possible that PHC degradation in biochar-amended soils is active and even enhanced under frozen conditions, but further investigation is required.
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Affiliation(s)
- Erin M Karppinen
- Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Katherine J Stewart
- Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Richard E Farrell
- Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Steven D Siciliano
- Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada; Toxicology Group, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada.
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49
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Jung W, Kim EJ, Han SJ, Kang SH, Choi HG, Kim S. Enzymatic modification by point mutation and functional analysis of an omega-6 fatty acid desaturase from Arctic Chlamydomonas sp. Prep Biochem Biotechnol 2017; 47:143-150. [PMID: 27191514 DOI: 10.1080/10826068.2016.1188311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Arctic Chlamydomonas sp. is a dominant microalgal strain in cold or frozen freshwater in the Arctic region. The full-length open reading frame of the omega-6 fatty acid desaturase gene (AChFAD6) was obtained from the transcriptomic database of Arctic Chlamydomonas sp. from the KOPRI culture collection of polar micro-organisms. Amino acid sequence analysis indicated the presence of three conserved histidine-rich segments as unique characteristics of omega-6 fatty acid desaturases, and three transmembrane regions transported to plastidic membranes by chloroplast transit peptides in the N-terminal region. The AChFAD6 desaturase activity was examined by expressing wild-type and V254A mutant (Mut-AChFAD6) heterologous recombinant proteins. Quantitative gas chromatography indicated that the concentration of linoleic acids in AChFAD6-transformed cells increased more than 3-fold [6.73 ± 0.13 mg g-1 dry cell weight (DCW)] compared with cells transformed with vector alone. In contrast, transformation with Mut-AChFAD6 increased the concentration of oleic acid to 9.23 ± 0.18 mg g-1 DCW, indicating a change in enzymatic activity to mimic that of stearoyl-CoA desaturase. These results demonstrate that AChFAD6 of Arctic Chlamydomonas sp. increases membrane fluidity by enhancing denaturation of C18 fatty acids and facilitates production of large quantities of linoleic fatty acids in prokaryotic expression systems.
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Affiliation(s)
- Woongsic Jung
- a Division of Polar Life Sciences, Korea Polar Research Institute , Korea Institute of Ocean Science and Technology , Incheon , Republic of Korea
| | - Eun Jae Kim
- a Division of Polar Life Sciences, Korea Polar Research Institute , Korea Institute of Ocean Science and Technology , Incheon , Republic of Korea.,b Department of Polar Life Sciences , University of Science and Technology , Incheon , Republic of Korea
| | - Se Jong Han
- a Division of Polar Life Sciences, Korea Polar Research Institute , Korea Institute of Ocean Science and Technology , Incheon , Republic of Korea.,b Department of Polar Life Sciences , University of Science and Technology , Incheon , Republic of Korea
| | - Sung-Ho Kang
- c Division of Polar Ocean Sciences, Korea Polar Research Institute , Korea Institute of Ocean Science and Technology , Incheon , Republic of Korea
| | - Han-Gu Choi
- a Division of Polar Life Sciences, Korea Polar Research Institute , Korea Institute of Ocean Science and Technology , Incheon , Republic of Korea
| | - Sanghee Kim
- a Division of Polar Life Sciences, Korea Polar Research Institute , Korea Institute of Ocean Science and Technology , Incheon , Republic of Korea
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50
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Nguyen V, Wilson C, Hoemberger M, Stiller JB, Agafonov RV, Kutter S, English J, Theobald DL, Kern D. Evolutionary drivers of thermoadaptation in enzyme catalysis. Science 2017; 355:289-294. [PMID: 28008087 PMCID: PMC5649376 DOI: 10.1126/science.aah3717] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/21/2016] [Indexed: 11/02/2022]
Abstract
With early life likely to have existed in a hot environment, enzymes had to cope with an inherent drop in catalytic speed caused by lowered temperature. Here we characterize the molecular mechanisms underlying thermoadaptation of enzyme catalysis in adenylate kinase using ancestral sequence reconstruction spanning 3 billion years of evolution. We show that evolution solved the enzyme's key kinetic obstacle-how to maintain catalytic speed on a cooler Earth-by exploiting transition-state heat capacity. Tracing the evolution of enzyme activity and stability from the hot-start toward modern hyperthermophilic, mesophilic, and psychrophilic organisms illustrates active pressure versus passive drift in evolution on a molecular level, refutes the debated activity/stability trade-off, and suggests that the catalytic speed of adenylate kinase is an evolutionary driver for organismal fitness.
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Affiliation(s)
- Vy Nguyen
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - Christopher Wilson
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - Marc Hoemberger
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - John B Stiller
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - Roman V Agafonov
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - Steffen Kutter
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - Justin English
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | | | - Dorothee Kern
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA.
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