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Choudhary P, Bhatt S, Chatterjee S. From freezing to functioning: cellular strategies of cold-adapted bacteria for surviving in extreme environments. Arch Microbiol 2024; 206:329. [PMID: 38940837 DOI: 10.1007/s00203-024-04058-5] [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: 04/09/2024] [Revised: 06/16/2024] [Accepted: 06/17/2024] [Indexed: 06/29/2024]
Abstract
The ability of cold-adapted bacteria to survive in extreme cold and diverse temperatures is due to their unique attributes like cell membrane stability, up-regulation of peptidoglycan biosynthesis, increased production of extracellular polymeric substances, and expansion of membrane pigment. Various cold-adapted proteins, including ice-nucleating proteins (INPs), antifreeze proteins (AFPs), cold shock proteins (Csps), and cold-acclimated proteins (CAPs), help the bacteria to survive in these environments. To sustain cells from extreme cold conditions and maintain stability in temperature fluctuations, survival strategies at the molecular level and their mechanism play significant roles in adaptations in cryospheric conditions. Furthermore, cold shock domains present in the multifunctional cold shock proteins play crucial roles in their adaptation strategies. The considerable contribution of lipopeptides, osmolytes, and membrane pigments plays an integral part in their survival in extreme environments. This review summarizes the evolutionary history of cold-adapted bacteria and their molecular and cellular adaptation strategies to thrive in harsh cold environments. It also discusses the importance of carotenoids produced, lipid composition, cryoprotectants, proteins, and chaperones related to this adaptation. Furthermore, the functions and mechanisms of adaptations within the cell are discussed briefly. One can utilize and explore their potential in various biotechnology applications and their evolutionary journey by knowing the inherent mechanism of their molecular and cellular adaptation to cold climatic conditions. This review will help all branches of the life science community understand the basic microbiology of psychrophiles and their hidden prospect in life science research.
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Affiliation(s)
- Priyanka Choudhary
- Bioremediation and Metabolomics Research Group, Department of Environmental Sciences, Central University of Himachal Pradesh, Academic Block-Shahpur, Kangra, Himachal Pradesh, 176206, India
| | - Sunidhi Bhatt
- Bioremediation and Metabolomics Research Group, Department of Environmental Sciences, Central University of Himachal Pradesh, Academic Block-Shahpur, Kangra, Himachal Pradesh, 176206, India
| | - Subhankar Chatterjee
- Bioremediation and Metabolomics Research Group, Dept. of Ecology & Environmental Sciences, School of Life Sciences, Pondicherry University, R.V. Nagar, Kalapet, Puducherry, 605014, 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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3
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Xiong L, Li Y, Yu H, Wei Y, Li H, Ji X. Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland. Sci Rep 2023; 13:14190. [PMID: 37648730 PMCID: PMC10468529 DOI: 10.1038/s41598-023-41323-x] [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: 01/02/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023] Open
Abstract
Microbial communities of wetlands play key roles in the earth's ecology and stability. To elucidate the cold adaptation mechanisms of bacteria in plateau wetlands, we conducted comparative genomic analyses of Pseudomonas sivasensis and closely related lineages. The genome of P. sivasensis W-6, a cold-adapted bacterium isolated from the Napahai plateau wetland, was sequenced and analyzed. The genome length was 6,109,123 bp with a G+C content of 59.5%. Gene prediction yielded 5360 protein-coding sequences, 70 tRNAs, 24 gene islands, and 2 CRISPR sequences. The isolate contained evidence of horizontal gene transfer events during its evolution. Two prophages were predicted and indicated that W-6 was a lysogen. The cold adaptation of the W-6 strain showed psychrophilic rather than psychrotrophic characteristics. Cold-adapted bacterium W-6 can utilize glycogen and trehalose as resources, associated with carbohydrate-active enzymes, and survive in a low-temperature environment. In addition, the cold-adapted mechanisms of the W-6 included membrane fluidity by changing the unsaturated fatty acid profile, the two-component regulatory systems, anti-sense transcription, the role played by rpsU genes in the translation process, etc. The genome-wide analysis of W-6 provided a deeper understanding of cold-adapted strategies of bacteria in environments. We elucidated the adaptive mechanism of the psychrophilic W-6 strain for survival in a cold environment, which provided a basis for further study on host-phage coevolution.
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Affiliation(s)
- Lingling Xiong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yanmei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Hang Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, China.
- Yunnan International Joint Laboratory of Research and Development of Crop Safety Production on Heavy Metal Pollution Areas, Kunming, China.
| | - Xiuling Ji
- Medical School, Kunming University of Science and Technology, Kunming, China.
- Yunnan International Joint Laboratory of Research and Development of Crop Safety Production on Heavy Metal Pollution Areas, Kunming, China.
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Dunn MF, Becerra-Rivera VA. The Biosynthesis and Functions of Polyamines in the Interaction of Plant Growth-Promoting Rhizobacteria with Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:2671. [PMID: 37514285 PMCID: PMC10385936 DOI: 10.3390/plants12142671] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/12/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023]
Abstract
Plant growth-promoting rhizobacteria (PGPR) are members of the plant rhizomicrobiome that enhance plant growth and stress resistance by increasing nutrient availability to the plant, producing phytohormones or other secondary metabolites, stimulating plant defense responses against abiotic stresses and pathogens, or fixing nitrogen. The use of PGPR to increase crop yield with minimal environmental impact is a sustainable and readily applicable replacement for a portion of chemical fertilizer and pesticides required for the growth of high-yielding varieties. Increased plant health and productivity have long been gained by applying PGPR as commercial inoculants to crops, although with uneven results. The establishment of plant-PGPR relationships requires the exchange of chemical signals and nutrients between the partners, and polyamines (PAs) are an important class of compounds that act as physiological effectors and signal molecules in plant-microbe interactions. In this review, we focus on the role of PAs in interactions between PGPR and plants. We describe the basic ecology of PGPR and the production and function of PAs in them and the plants with which they interact. We examine the metabolism and the roles of PAs in PGPR and plants individually and during their interaction with one another. Lastly, we describe some directions for future research.
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Affiliation(s)
- Michael F Dunn
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Víctor A Becerra-Rivera
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
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5
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Marian M, Licciardello G, Vicelli B, Pertot I, Perazzolli M. Ecology and potential functions of plant-associated microbial communities in cold environments. FEMS Microbiol Ecol 2022; 98:fiab161. [PMID: 34910139 PMCID: PMC8769928 DOI: 10.1093/femsec/fiab161] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
Complex microbial communities are associated with plants and can improve their resilience under harsh environmental conditions. In particular, plants and their associated communities have developed complex adaptation strategies against cold stress. Although changes in plant-associated microbial community structure have been analysed in different cold regions, scarce information is available on possible common taxonomic and functional features of microbial communities across cold environments. In this review, we discuss recent advances in taxonomic and functional characterization of plant-associated microbial communities in three main cold regions, such as alpine, Arctic and Antarctica environments. Culture-independent and culture-dependent approaches are analysed, in order to highlight the main factors affecting the taxonomic structure of plant-associated communities in cold environments. Moreover, biotechnological applications of plant-associated microorganisms from cold environments are proposed for agriculture, industry and medicine, according to biological functions and cold adaptation strategies of bacteria and fungi. Although further functional studies may improve our knowledge, the existing literature suggest that plants growing in cold environments harbor complex, host-specific and cold-adapted microbial communities, which may play key functional roles in plant growth and survival under cold conditions.
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Affiliation(s)
- Malek Marian
- Center Agriculture Food Environment (C3A), University of Trento, via E. Mach 1, 38098 San Michele all'Adige, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Giorgio Licciardello
- Center Agriculture Food Environment (C3A), University of Trento, via E. Mach 1, 38098 San Michele all'Adige, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Bianca Vicelli
- Center Agriculture Food Environment (C3A), University of Trento, via E. Mach 1, 38098 San Michele all'Adige, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Ilaria Pertot
- Center Agriculture Food Environment (C3A), University of Trento, via E. Mach 1, 38098 San Michele all'Adige, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Michele Perazzolli
- Center Agriculture Food Environment (C3A), University of Trento, via E. Mach 1, 38098 San Michele all'Adige, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy
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Shen L, Zhang S, Chen G. Regulated strategies of cold-adapted microorganisms in response to cold: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:68006-68024. [PMID: 34648167 DOI: 10.1007/s11356-021-16843-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
There are a large number of active cold-adapted microorganisms in the perennial cold environment. Due to their high-efficiency and energy-saving catalytic properties, cold-adapted microorganisms have become valuable natural resources with potential in various biological fields. In this study, a series of cold response strategies for microorganisms were summarized. This mainly involves the regulation of cell membrane fluidity, synthesis of cold adaptation proteins, regulators and metabolic changes, energy supply, and reactive oxygen species. Also, the potential of biocatalysts produced by cold-adapted microorganisms including cold-active enzymes, ice-binding proteins, polyhydroxyalkanoates, and surfactants was introduced, which provided a guidance for expanding its application values. Overall, new insights were obtained on response strategies of microorganisms to cold environments in this review. This will deepen the understanding of the cold tolerance mechanism of cold-adapted microorganisms, thus promoting the establishment and application of low-temperature biotechnology.
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Affiliation(s)
- Lijun Shen
- College of Life Sciences, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Biology and Utilization, The Ministry of Education, Changchun, China
| | - Sitong Zhang
- College of Life Sciences, Jilin Agricultural University, Changchun, China.
- Key Laboratory of Straw Biology and Utilization, The Ministry of Education, Changchun, China.
| | - Guang Chen
- College of Life Sciences, Jilin Agricultural University, Changchun, China.
- Key Laboratory of Straw Biology and Utilization, The Ministry of Education, Changchun, China.
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Hu X, Tang X, Bi Z, Zhao Q, Ren L. Adaptive evolution of microalgae Schizochytrium sp. under high temperature for efficient production of docosahexaeonic acid. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Complete genome sequencing of Bacillus sp. TK-2, analysis of its cold evolution adaptability. Sci Rep 2021; 11:4836. [PMID: 33649356 PMCID: PMC7921382 DOI: 10.1038/s41598-021-84286-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 02/15/2021] [Indexed: 12/23/2022] Open
Abstract
To date, a large number of Bacillus species from different sources have been identified. However, there are few investigations on genome information and evolutionary insights of Bacillus species from cold environments. Bacillus sp. TK-2, isolated from the soil of Changbai Mountain, is a gram-positive bacterium with cold adaptation characteristics. In this study, we present the annotated complete genome sequence of Bacillus sp. TK-2. The genome comprised 5,286,177 bp with a GC content of 35.88%, 5293 protein-encoding genes, 32 rRNA, and 77 tRNA. Numerous genes related to cold adaptation were detected in the genome of Bacillus sp. TK-2, mainly involving in energy supply, regulation of cell membrane fluidity, antioxidant, and molecular chaperones. In addition, the strain TK-2 classified in the Bacillus groups was distributed on a terminal branch with Bacillus cereus A1 by Blastn and phylogenetic analysis in NCBI database. Complete genome sequences of the strain TK-2 and Bacillus cereus A1 were compared by the online tool "Average Nucleotide Identity", showing that the average nucleotide identity of these two strains was 98.26%. In parallel, A comparative analysis of the genomes of both Bacillus sp. TK-2 and Bacillus cereus A1 was conducted. Through the analysis of core and specific genes with cd-hit, it was found that the two strains had 5691 pan gene, 4524 core gene, and 1167 specific gene clusters. Among the 624 specific gene clusters of Bacillus sp. TK-2, some cold tolerance genes were detected, which implied the unique adaptability of Bacillus sp. TK-2 in long-term low temperature environments. Importantly, enzyme-encoding genes related to the degradation of polysaccharides such as cellulose and hemicellulose were detected in the 477 CAZyme genes of this genome. This work on sequencing and bioinformatics analysis of the complete sequence of Bacillus sp. TK-2 promote the application and in-depth research of low-temperature biotechnology.
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TMT-Based Quantitative Proteomics Analysis of the Fish-Borne Spoiler Shewanella putrefaciens Subjected to Cold Stress Using LC-MS/MS. J CHEM-NY 2021. [DOI: 10.1155/2021/8876986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Shewanella putrefaciens is a specific spoilage bacterium for fish during cold storage. To better understand the molecular mechanisms of cold stress adaptation of S. putrefaciens, tandem mass tag- (TMT-) based quantitative proteomic analysis was performed to detect the effects of cold stress on protein expression profiles in S. putrefaciens which had been cultivated at 4°C and 30°C, respectively. A total of 266670 peptide spectrum matching numbers were quantified proteins after data analysis. Of the 2292 proteins quantitatively analyzed, a total of 274 were found to be differentially expressed (DE) under cold stress compared with the nonstress control. By integrating the results of Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, 9 common KEGG terms were found notable for the cold-responsive proteins. Generally, the DE proteins involved in carbohydrate, amino acid, and fatty acid biosynthesis and metabolism were significantly upregulated, leading to a specific energy conservation survival mode. The DE proteins related to DNA repair, transcription, and translation were upregulated, implicating change of gene expression and more protein biosynthesis needed in response to cold stress.
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Safronova VI, Guro PV, Sazanova AL, Kuznetsova IG, Belimov AA, Yakubov VV, Chirak ER, Afonin AМ, Gogolev YV, Andronov EE, Tikhonovich IA. Rhizobial Microsymbionts of Kamchatka Oxytropis Species Possess Genes of the Type III and VI Secretion Systems, Which Can Affect the Development of Symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1232-1241. [PMID: 32686981 DOI: 10.1094/mpmi-05-20-0114-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A collection of rhizobial strains isolated from root nodules of the narrowly endemic legume species Oxytropis erecta, O. anadyrensis, O. kamtschatica, and O. pumilio originating from the Kamchatka Peninsula (Russian Federation) was obtained. Analysis of the 16S ribosomal RNA gene sequence showed a significant diversity of isolates belonging to families Rhizobiaceae (genus Rhizobium), Phyllobacteriaceae (genera Mesorhizobium, Phyllobacterium), and Bradyrhizobiaceae (genera Bosea, Tardiphaga). A plant nodulation assay showed that only strains belonging to genus Mesorhizobium could form nitrogen-fixing nodules on Oxytropis plants. The strains M. loti 582 and M. huakuii 583, in addition to symbiotic clusters, possessed genes of the type III and type VI secretion systems (T3SS and T6SS, respectively), which can influence the host specificity of strains. These strains formed nodules of two types (elongated and rounded) on O. kamtschatica roots. We suggest this phenomenon may result from Nod factor-dependent and -independent nodulation strategies. The obtained strains are of interest for further study of the T3SS and T6SS gene function and their role in the development of rhizobium-legume symbiosis. The prospects of using rhizobia having both gene systems related to symbiotic and nonsymbiotic nodulation strategies to enhance the efficiency of plant-microbe interactions by expanding the host specificity and increasing nodulation efficiency are discussed.
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Affiliation(s)
- Vera I Safronova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St.-Petersburg, Sh. Podbelskogo 3, Russian Federation
| | - Polina V Guro
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St.-Petersburg, Sh. Podbelskogo 3, Russian Federation
| | - Anna L Sazanova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St.-Petersburg, Sh. Podbelskogo 3, Russian Federation
| | - Irina G Kuznetsova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St.-Petersburg, Sh. Podbelskogo 3, Russian Federation
| | - Andrey A Belimov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St.-Petersburg, Sh. Podbelskogo 3, Russian Federation
| | - Valentin V Yakubov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the RAS, 690022, Vladivostok, Ave. 100-let Vladivostoka 159, Russian Federation
| | - Elizaveta R Chirak
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St.-Petersburg, Sh. Podbelskogo 3, Russian Federation
| | - Alexey М Afonin
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St.-Petersburg, Sh. Podbelskogo 3, Russian Federation
| | - Yuri V Gogolev
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 2/31 Lobachevsky St., Kazan 420111, Russian Federation
| | - Evgeny E Andronov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St.-Petersburg, Sh. Podbelskogo 3, Russian Federation
| | - Igor A Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St.-Petersburg, Sh. Podbelskogo 3, Russian Federation
- Saint Petersburg State University, Department of Genetics and Biotechnology, 199034, St.-Petersburg, Universitetskaya Emb. 7/9, Russian Federation
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11
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Yi Z, Cao X, Li H, Jian H, Xu X, Yu L, Tang X. Genomic analysis of Microbacterium sediminis YLB-01 T reveals backgrounds related to its deep-sea environment adaptation. Mar Genomics 2020; 56:100818. [PMID: 33632425 DOI: 10.1016/j.margen.2020.100818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 08/14/2020] [Accepted: 08/27/2020] [Indexed: 11/27/2022]
Abstract
Microbacterium sediminis YLB-01T, a piezotolerant and psychrotolerant actinomycete, was isolated from deep-sea sediment of the South-West Indian Ocean and could be a good model for understanding the adaptation of extremophiles to the benthic piezosphere. Here, we report the analysis of the complete genome sequence of strain YLB-01T. The genome sequence consists of a single circular chromosome comprising 2,792,195 bp and a linear plasmid comprising 127,669 bp with G + C content of 71.76 and 68.49 mol%, respectively. In this regard, strain YLB-01T possesses the smallest genome size but the highest G + C content among the genus Microbacterium sequenced to date. As the first complete genome sequence of the genus Microbacterium isolated from deep-sea environment, the strain YLB-01T genome is unique or enriched in genes involved in xenobiotics biodegradation and metabolism, compatible solutes, and transposases, some of which might be related to bacterial enhancement of ecological fitness in the deep sea.
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Affiliation(s)
- Zhiwei Yi
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Xiaorong Cao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Hong Li
- China National Accreditation Insititute for Conformity Assessment, No. 8 Nanhuashi Dajie Chongwen District, Beijing 10086, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiashutong Xu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Libo Yu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Xixiang Tang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; China Ocean Sample Respository (Biology), Xiamen 361005, China.
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12
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Sajjad W, Din G, Rafiq M, Iqbal A, Khan S, Zada S, Ali B, Kang S. Pigment production by cold-adapted bacteria and fungi: colorful tale of cryosphere with wide range applications. Extremophiles 2020; 24:447-473. [PMID: 32488508 PMCID: PMC7266124 DOI: 10.1007/s00792-020-01180-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/18/2020] [Indexed: 12/18/2022]
Abstract
Pigments are an essential part of everyday life on Earth with rapidly growing industrial and biomedical applications. Synthetic pigments account for a major portion of these pigments that in turn have deleterious effects on public health and environment. Such drawbacks of synthetic pigments have shifted the trend to use natural pigments that are considered as the best alternative to synthetic pigments due to their significant properties. Natural pigments from microorganisms are of great interest due to their broader applications in the pharmaceutical, food, and textile industry with increasing demand among the consumers opting for natural pigments. To fulfill the market demand of natural pigments new sources should be explored. Cold-adapted bacteria and fungi in the cryosphere produce a variety of pigments as a protective strategy against ecological stresses such as low temperature, oxidative stresses, and ultraviolet radiation making them a potential source for natural pigment production. This review highlights the protective strategies and pigment production by cold-adapted bacteria and fungi, their industrial and biomedical applications, condition optimization for maximum pigment extraction as well as the challenges facing in the exploitation of cryospheric microorganisms for pigment extraction that hopefully will provide valuable information, direction, and progress in forthcoming studies.
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Affiliation(s)
- Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Ghufranud Din
- Department of Microbiology, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta, Pakistan
| | - Awais Iqbal
- School of Life Sciences, State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Lanzhou, People's Republic of China
| | - Suliman Khan
- The Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Sahib Zada
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Barkat Ali
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Shichang Kang
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing, China.
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13
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Psychrophilic lifestyles: mechanisms of adaptation and biotechnological tools. Appl Microbiol Biotechnol 2019; 103:2857-2871. [PMID: 30729286 DOI: 10.1007/s00253-019-09659-5] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 12/22/2022]
Abstract
Cold-adapted microorganisms inhabiting permanently low-temperature environments were initially just a biological curiosity but have emerged as rich sources of numerous valuable tools for application in a broad spectrum of innovative technologies. To overcome the multiple challenges inherent to life in their cold habitats, these microorganisms have developed a diverse array of highly sophisticated synergistic adaptations at all levels within their cells: from cell envelope and enzyme adaptation, to cryoprotectant and chaperone production, and novel metabolic capabilities. Basic research has provided valuable insights into how these microorganisms can thrive in their challenging habitat conditions and into the mechanisms of action of the various adaptive features employed, and such insights have served as a foundation for the knowledge-based development of numerous novel biotechnological tools. In this review, we describe the current knowledge of the adaptation strategies of cold-adapted microorganisms and the biotechnological perspectives and commercial tools emerging from this knowledge. Adaptive features and, where possible, applications, in relation to membrane fatty acids, membrane pigments, the cell wall peptidoglycan layer, the lipopolysaccharide component of the outer cell membrane, compatible solutes, antifreeze and ice-nucleating proteins, extracellular polymeric substances, biosurfactants, chaperones, storage materials such as polyhydroxyalkanoates and cyanophycins and metabolic adjustments are presented and discussed.
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diCenzo GC, Zamani M, Checcucci A, Fondi M, Griffitts JS, Finan TM, Mengoni A. Multidisciplinary approaches for studying rhizobium–legume symbioses. Can J Microbiol 2019; 65:1-33. [DOI: 10.1139/cjm-2018-0377] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The rhizobium–legume symbiosis is a major source of fixed nitrogen (ammonia) in the biosphere. The potential for this process to increase agricultural yield while reducing the reliance on nitrogen-based fertilizers has generated interest in understanding and manipulating this process. For decades, rhizobium research has benefited from the use of leading techniques from a very broad set of fields, including population genetics, molecular genetics, genomics, and systems biology. In this review, we summarize many of the research strategies that have been employed in the study of rhizobia and the unique knowledge gained from these diverse tools, with a focus on genome- and systems-level approaches. We then describe ongoing synthetic biology approaches aimed at improving existing symbioses or engineering completely new symbiotic interactions. The review concludes with our perspective of the future directions and challenges of the field, with an emphasis on how the application of a multidisciplinary approach and the development of new methods will be necessary to ensure successful biotechnological manipulation of the symbiosis.
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Affiliation(s)
- George C. diCenzo
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Maryam Zamani
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alice Checcucci
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Marco Fondi
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Joel S. Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Turlough M. Finan
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
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Abstract
It is well known that cold environments are predominant over the Earth and there are a great number of reports analyzing bacterial adaptations to cold. Most of these works are focused on characteristics traditionally involved in cold adaptation, such as the structural adjustment of enzymes, maintenance of membrane fluidity, expression of cold shock proteins and presence of compatible solutes. Recent works based mainly on novel "omic" technologies have presented evidence of the presence of other important features to thrive in cold. In this work, we analyze cold-adapted bacteria, looking for strategies involving novel features, and/or activation of non-classical metabolisms for a cold lifestyle. Metabolic traits related to energy generation, compounds and mechanisms involved in stress resistance and cold adaptation, as well as characteristics of the cell envelope, are analyzed in heterotrophic cold-adapted bacteria. In addition, metagenomic, metatranscriptomic and metaproteomic data are used to detect key functions in bacterial communities inhabiting cold environments.
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Affiliation(s)
- Paula M Tribelli
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina.
- IQUIBICEN, CONICET, C1428EGA Buenos Aires, Argentina.
| | - Nancy I López
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina.
- IQUIBICEN, CONICET, C1428EGA Buenos Aires, Argentina.
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Koo H, Hakim JA, Morrow CD, Andersen DT, Bej AK. Microbial Community Composition and Predicted Functional Attributes of Antarctic Lithobionts Using Targeted Next-Generation Sequencing and Bioinformatics Tools. J Microbiol Methods 2018. [DOI: 10.1016/bs.mim.2018.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Genomic insights into temperature-dependent transcriptional responses of Kosmotoga olearia, a deep-biosphere bacterium that can grow from 20 to 79 °C. Extremophiles 2017; 21:963-979. [PMID: 28894932 PMCID: PMC5674127 DOI: 10.1007/s00792-017-0956-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/11/2017] [Indexed: 11/29/2022]
Abstract
Temperature is one of the defining parameters of an ecological niche. Most organisms thrive within a temperature range that rarely exceeds ~30 °C, but the deep subsurface bacterium Kosmotoga olearia can grow over a temperature range of 59 °C (20–79 °C). To identify genes correlated with this flexible phenotype, we compared transcriptomes of K. olearia cultures grown at its optimal 65 °C to those at 30, 40, and 77 °C. The temperature treatments affected expression of 573 of 2224 K. olearia genes. Notably, this transcriptional response elicits re-modeling of the cellular membrane and changes in metabolism, with increased expression of genes involved in energy and carbohydrate metabolism at high temperatures and up-regulation of amino acid metabolism at lower temperatures. At sub-optimal temperatures, many transcriptional changes were similar to those observed in mesophilic bacteria at physiologically low temperatures, including up-regulation of typical cold stress genes and ribosomal proteins. Comparative genomic analysis of additional Thermotogae genomes indicates that one of K. olearia’s strategies for low-temperature growth is increased copy number of some typical cold response genes through duplication and/or lateral acquisition. At 77 °C one-third of the up-regulated genes are of hypothetical function, indicating that many features of high-temperature growth are unknown.
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Sierra EM, Pereira MR, Maester TC, Gomes-Pepe ES, Mendoza ER, Lemos EGDM. Halotolerant aminopeptidase M29 from Mesorhizobium SEMIA 3007 with biotechnological potential and its impact on biofilm synthesis. Sci Rep 2017; 7:10684. [PMID: 28878230 PMCID: PMC5587760 DOI: 10.1038/s41598-017-10932-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/16/2017] [Indexed: 12/04/2022] Open
Abstract
The aminopeptidase gene from Mesorhizobium SEMIA3007 was cloned and overexpressed in Escherichia coli. The enzyme called MesoAmp exhibited optimum activity at pH 8.5 and 45 °C and was strongly activated by Co2+ and Mn2+. Under these reaction conditions, the enzyme displayed Km and kcat values of 0.2364 ± 0.018 mM and 712.1 ± 88.12 s−1, respectively. Additionally, the enzyme showed remarkable stability in organic solvents and was active at high concentrations of NaCl, suggesting that the enzyme might be suitable for use in biotechnology. MesoAmp is responsible for 40% of the organism’s aminopeptidase activity. However, the enzyme’s absence does not affect bacterial growth in synthetic broth, although it interfered with biofilm synthesis and osmoregulation. To the best of our knowledge, this report describes the first detailed characterization of aminopeptidase from Mesorhizobium and suggests its importance in biofilm formation and osmotic stress tolerance. In summary, this work lays the foundation for potential biotechnological applications and/or the development of environmentally friendly technologies and describes the first solvent- and halo-tolerant aminopeptidases identified from the Mesorhizobium genus and its importance in bacterial metabolism.
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Affiliation(s)
- Elwi Machado Sierra
- Department of Technology, São Paulo State University, Jaboticabal, São Paulo State, Brazil.,Universidad Simón Bolívar, Barranquilla, Colombia
| | | | | | - Elisangela Soares Gomes-Pepe
- Department of Technology, São Paulo State University, Jaboticabal, São Paulo State, Brazil.,Institute for Research in Bioenergy (IPBEN), Jaboticabal, São Paulo State, Brazil
| | - Elkin Rodas Mendoza
- Department of Technology, São Paulo State University, Jaboticabal, São Paulo State, Brazil
| | - Eliana G de Macedo Lemos
- Department of Technology, São Paulo State University, Jaboticabal, São Paulo State, Brazil. .,Institute for Research in Bioenergy (IPBEN), Jaboticabal, São Paulo State, Brazil. .,Av. Prof. Paulo Donato Castellane, s/n. Jaboticabal, Post code 14884-900, São Paulo State, Brazil.
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Baraúna RA, Freitas DY, Pinheiro JC, Folador ARC, Silva A. A Proteomic Perspective on the Bacterial Adaptation to Cold: Integrating OMICs Data of the Psychrotrophic Bacterium Exiguobacterium antarcticum B7. Proteomes 2017; 5:proteomes5010009. [PMID: 28248259 PMCID: PMC5372230 DOI: 10.3390/proteomes5010009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/24/2016] [Accepted: 12/05/2016] [Indexed: 11/30/2022] Open
Abstract
Since the publication of one of the first studies using 2D gel electrophoresis by Patrick H. O’Farrell in 1975, several other studies have used that method to evaluate cellular responses to different physicochemical variations. In environmental microbiology, bacterial adaptation to cold environments is a “hot topic” because of its application in biotechnological processes. As in other fields, gel-based and gel-free proteomic methods have been used to determine the molecular mechanisms of adaptation to cold of several psychrotrophic and psychrophilic bacterial species. In this review, we aim to describe and discuss these main molecular mechanisms of cold adaptation, referencing proteomic studies that have made significant contributions to our current knowledge in the area. Furthermore, we use Exiguobacterium antarcticum B7 as a model organism to present the importance of integrating genomic, transcriptomic, and proteomic data. This species has been isolated in Antarctica and previously studied at all three omic levels. The integration of these data permitted more robust conclusions about the mechanisms of bacterial adaptation to cold.
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Affiliation(s)
- Rafael A Baraúna
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil.
| | - Dhara Y Freitas
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil.
| | - Juliana C Pinheiro
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil.
| | - Adriana R C Folador
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil.
| | - Artur Silva
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil.
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