151
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Santos-Merino M, Singh AK, Ducat DC. New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering. Front Bioeng Biotechnol 2019; 7:33. [PMID: 30873404 PMCID: PMC6400836 DOI: 10.3389/fbioe.2019.00033] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/05/2019] [Indexed: 01/25/2023] Open
Abstract
Cyanobacteria are promising microorganisms for sustainable biotechnologies, yet unlocking their potential requires radical re-engineering and application of cutting-edge synthetic biology techniques. In recent years, the available devices and strategies for modifying cyanobacteria have been increasing, including advances in the design of genetic promoters, ribosome binding sites, riboswitches, reporter proteins, modular vector systems, and markerless selection systems. Because of these new toolkits, cyanobacteria have been successfully engineered to express heterologous pathways for the production of a wide variety of valuable compounds. Cyanobacterial strains with the potential to be used in real-world applications will require the refinement of genetic circuits used to express the heterologous pathways and development of accurate models that predict how these pathways can be best integrated into the larger cellular metabolic network. Herein, we review advances that have been made to translate synthetic biology tools into cyanobacterial model organisms and summarize experimental and in silico strategies that have been employed to increase their bioproduction potential. Despite the advances in synthetic biology and metabolic engineering during the last years, it is clear that still further improvements are required if cyanobacteria are to be competitive with heterotrophic microorganisms for the bioproduction of added-value compounds.
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Affiliation(s)
- María Santos-Merino
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - Amit K. Singh
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - Daniel C. Ducat
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
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152
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Ren F, Dong W, Yan DH. Endophytic bacterial communities of Jingbai Pear trees in north China analyzed with Illumina sequencing of 16S rDNA. Arch Microbiol 2018; 201:199-208. [PMID: 30506399 DOI: 10.1007/s00203-018-1597-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/05/2018] [Accepted: 11/16/2018] [Indexed: 01/08/2023]
Abstract
Plant endophytes play a crucial role in plant growth, health and ecological function. Jingbai pear (the best quality cultivar of Pyrus ussuriensi Maxim. ex Rupr.) has important ecological and economic value in north China. Conversation of its genetics has great meanings to pear genus (Pyrus L.). However, the bacterial community associated with the cultivar remains unknown. In this study, the structure of endophytic bacterial communities associated with different tissues and soil of Jingbai Pear trees was analyzed with Illumina Miseq sequencing of bacterial 16S rDNA. This is the first report on bacterial microbiome associated with Jingbai pear. Our results demonstrated that different tissues harbored a unique bacterial assemblage. Interestingly, Cyanobacteria was the most abundant phylum, followed by Proteobacteria and Actinobacteria. Samples from three different sites (soils) had significant differences in microbial communities structure. Redundancy analysis (RDA) showed that the bacterial community structure correlated significantly with soil properties-temperature, pH, nitrogen and carbon contents. The conclusion could facilitate to understand the interaction and ecological function of endophytic bacteria with host Jingbai pear trees, so as to benefit the pear variety genetic resource conservation and protection.
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Affiliation(s)
- Fei Ren
- Forestry Experiment Center in North China, Chinese Academy of Forestry, Beijing, 102300, China.
| | - Wei Dong
- China Electric Power Research Institute, Beijing, 100192, China
| | - Dong-Hui Yan
- The Key Laboratory of Forest Protection Affiliated to State Forestry Administration of China, Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, 100091, China.
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153
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Singh AK, Singh PP, Tripathi V, Verma H, Singh SK, Srivastava AK, Kumar A. Distribution of cyanobacteria and their interactions with pesticides in paddy field: A comprehensive review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 224:361-375. [PMID: 30059934 DOI: 10.1016/j.jenvman.2018.07.039] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/13/2018] [Accepted: 07/14/2018] [Indexed: 06/08/2023]
Abstract
Cyanobacteria, also known as blue green algae are one of the important ubiquitous oxygen evolving photosynthetic prokaryotes and ultimate source of nitrogen for paddy fields since decades. In past two decades, indiscriminated use of pesticides led to biomagnification that intensively harm the structure and soil functions of soil microbes including cyanobacteria. Cyanobacterial abundance biomass, short generation, water holding capacity, mineralizing capacity and more importantly nitrogen fixing have enormous potential to abate the negative effects of pesticides. Therefore, investigation of the ecotoxicological effects of pesticides on the structure and function of the tropical paddy field associated cyanobacteria is urgent and need to estimate the fate of interaction of pesticides over nitrogen fixations and other attributes. In this regard, comprehensive survey over cyanobacterial distribution patterns and their interaction with pesticides in Indian context has been deeply reviewed. In addition, the present paper also deals the molecular docking pattern of pesticides with the nitrogen fixing proteins, which helps in revealing the functional interpretation over nitrogen fixation process.
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Affiliation(s)
| | - Prem Pratap Singh
- Center of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Vijay Tripathi
- Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, 211007, India
| | - Hariom Verma
- Center of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Sandeep Kumar Singh
- Center of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | | | - Ajay Kumar
- Center of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
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154
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Tiwari S, Patel A, Prasad SM. Kinetin alleviates chromium toxicity on growth and PS II photochemistry in Nostoc muscorum by regulating antioxidant system. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 161:296-304. [PMID: 29890431 DOI: 10.1016/j.ecoenv.2018.05.052] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 05/20/2018] [Accepted: 05/22/2018] [Indexed: 06/08/2023]
Abstract
The present study was undertaken to evaluate the metal toxicity alleviating effects of kinetin (KN, 10 nM) on growth, photosynthetic pigments and photochemistry of PS II in the cyanobacterium Nostoc muscorum exposed to chromium (CrVI) stress (100 and 150 µM). Chromium declined growth, photosynthetic pigments (chlorophyll a, phycocyanin and carotenoids), photosynthetic oxygen evolution rate and parameters of fluorescence kinetics (ϕP0, FV/F0, ϕE0, Ψ0 and PIABS except F0/FV) in concentration dependent manner, while stimulating effects on respiration, energy flux parameters (ABS/RC, TR0/RC, ET0/RC and DI0/RC), oxidative stress biomarkers i.e., superoxide radical (SOR), hydrogen peroxide (H2O2) and lipid peroxidation (TBARS contents) and antioxidative enzymes: superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and glutathione-S-transferase (GST), were observed. However, upon addition of KN in the growth medium an alleviating effect against chromium induced toxicity on growth, photosynthetic pigments and photochemistry of PS II was recorded. This had occurred due to substantial reduction in levels of oxidative stress biomarkers: SOR, H2O2 and TBARS contents with concomitant rise in activity of antioxidative enzymes: SOD, POD, CAT and GST and appreciable lowering in the cellular accumulation of chromium. The overall results demonstrate that KN application significantly alleviated chromium induced toxicity on growth performance of the cyanobacterium N. muscorum due to significant improvement in photosynthetic pigments and photochemistry of PS II by up-regulating the activity of antioxidative enzymes, and declining cellular accumulation of chromium. Furthermore, Cr induced toxicity at lower dose (100 µM) was found to be ameliorated more efficiently in N. muscorum following supplementation of KN.
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Affiliation(s)
- Sanjesh Tiwari
- Ranjan Plant physiology and Biochemistry Laboratory, Department of Botany, University of Allahabad, Allahabad 211002, India
| | - Anuradha Patel
- Ranjan Plant physiology and Biochemistry Laboratory, Department of Botany, University of Allahabad, Allahabad 211002, India
| | - Sheo Mohan Prasad
- Ranjan Plant physiology and Biochemistry Laboratory, Department of Botany, University of Allahabad, Allahabad 211002, India.
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155
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Muñoz-Rojas M, Román JR, Roncero-Ramos B, Erickson TE, Merritt DJ, Aguila-Carricondo P, Cantón Y. Cyanobacteria inoculation enhances carbon sequestration in soil substrates used in dryland restoration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 636:1149-1154. [PMID: 29913577 DOI: 10.1016/j.scitotenv.2018.04.265] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/19/2018] [Accepted: 04/20/2018] [Indexed: 06/08/2023]
Abstract
Despite significant efforts to restore dryland ecosystems worldwide, the rate of success of restoration is extremely low in these areas. The role of cyanobacteria from soil biocrusts in reestablishing soil functions of degraded land has been highlighted in recent years. These organisms are capable of improving soil structure and promoting soil N and C fixation. Nevertheless, their application to restore functions of reconstructed soils in dryland restoration programs is yet to be harnessed. In this study, we used microcosms under laboratory conditions to analyse the effects of inoculating soil substrates used in post-mine restoration with a mixture of N-fixing cyanobacteria isolated from soil biocrust (Nostoc commune, Tolypothrix distorta and Scytonema hyalinum) on i) the recovery of the biocrust, and ii) the carbon sequestration and mineralisation rates of these substrates. Soils were collected from an active mine site in the mining-intensive biodiverse Pilbara region (north-west Western Australia) and consisted of previously stockpiled topsoil, overburden waste material, a mixture of both substrates, and a natural soil from an undisturbed area. Our results showed that cyanobacteria rapidly colonised the mine substrates, with biocrust coverage ranging from 23.8 to 52.2% and chlorophyll a concentrations of up to 12.2 μg g-1 three months after inoculation. Notably, soil organic C contents increased 3-fold (P < 0.001) in the mine waste substrate (from 0.6 g kg-1 to 1.9 g kg-1) during this period of time. Overall, our results showed that cyanobacteria inoculation can rapidly modify properties of reconstructed soil substrates, underpinning the potential key role of these organisms as bio-tools to initiate recovery of soil functions in infertile, reconstructed soil substrates.
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Affiliation(s)
- M Muñoz-Rojas
- The University of Western Australia, School of Biological Sciences, Crawley 6009, WA, Australia; Kings Park Science, Department of Biodiversity, Conservation and Attractions, Kings Park, 6005, WA, Australia; University of New South Wales, School of Biological, Earth & Environmental Sciences, Sydney 2052, NSW, Australia.
| | - J R Román
- University of Almería, Agronomy Department, 04120 Almería, Spain
| | - B Roncero-Ramos
- University of Almería, Agronomy Department, 04120 Almería, Spain
| | - T E Erickson
- The University of Western Australia, School of Biological Sciences, Crawley 6009, WA, Australia; Kings Park Science, Department of Biodiversity, Conservation and Attractions, Kings Park, 6005, WA, Australia
| | - D J Merritt
- The University of Western Australia, School of Biological Sciences, Crawley 6009, WA, Australia; Kings Park Science, Department of Biodiversity, Conservation and Attractions, Kings Park, 6005, WA, Australia
| | | | - Y Cantón
- University of Almería, Agronomy Department, 04120 Almería, Spain
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156
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Singh JS, Gupta VK. Soil microbial biomass: A key soil driver in management of ecosystem functioning. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 634:497-500. [PMID: 29635193 DOI: 10.1016/j.scitotenv.2018.03.373] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/30/2018] [Accepted: 03/30/2018] [Indexed: 05/20/2023]
Abstract
Although patterns of microbial diversity and biomass have been described and reviewed at local and regional scales, a unifying driver, or set of environmental drivers affecting soil microbial biomass (SMB) pattern at global level is still missing. Biomass of soil microbial community, known as SMB is considered widely as the index of soil fertility and ecosystem productivity. The escalating soil stresses due to land degradation and climatic variability are directly correlated with loss of microbial diversity and abundance or biomass dynamics. Therefore, alleviating soil stresses on microbial communities with ecological restoration could reduce the unpredictability and turnover rates of SMB. Thus, the key ecological factors which stabilize the SMB and minimize its turnover, are supposed to play an important role in the soil nutrient dynamics and productivity of the ecosystems. Because of the existing public concern about the deleterious impacts of ecosystem degradation, there is an increasing interest in improving the understanding of SMB, and the way, it contributes to restoration and functioning of ecosystems.
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Affiliation(s)
- Jay Shankar Singh
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar (Central) University, Raebarelly Road, Lucknow 226025, Uttar Pradesh, India.
| | - Vijai Kumar Gupta
- Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, School of Science, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
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157
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Win TT, Barone GD, Secundo F, Fu P. Algal Biofertilizers and Plant Growth Stimulants for Sustainable Agriculture. Ind Biotechnol (New Rochelle N Y) 2018. [DOI: 10.1089/ind.2018.0010] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Theint Theint Win
- State Key Laboratory of Marine Resource Utilization in South China, Hainan University, Haikou, China
- Biotechnology Research Department, Ministry of Education, Kyaukse, Mandalay, Myanmar
| | | | - Francesco Secundo
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Pengcheng Fu
- State Key Laboratory of Marine Resource Utilization in South China, Hainan University, Haikou, China
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158
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Sabri NSA, Zakaria Z, Mohamad SE, Jaafar AB, Hara H. Importance of Soil Temperature for the Growth of Temperate Crops under a Tropical Climate and Functional Role of Soil Microbial Diversity. Microbes Environ 2018; 33:144-150. [PMID: 29709895 PMCID: PMC6031386 DOI: 10.1264/jsme2.me17181] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/16/2018] [Indexed: 11/17/2022] Open
Abstract
A soil cooling system that prepares soil for temperate soil temperatures for the growth of temperate crops under a tropical climate is described herein. Temperate agriculture has been threatened by the negative impact of temperature increases caused by climate change. Soil temperature closely correlates with the growth of temperate crops, and affects plant processes and soil microbial diversity. The present study focuses on the effects of soil temperatures on lettuce growth and soil microbial diversity that maintains the growth of lettuce at low soil temperatures. A model temperate crop, loose leaf lettuce, was grown on eutrophic soil under soil cooling and a number of parameters, such as fresh weight, height, the number of leaves, and root length, were evaluated upon harvest. Under soil cooling, significant differences were observed in the average fresh weight (P<0.05) and positive development of the roots, shoots, and leaves of lettuce. Janthinobacterium (8.142%), Rhodoplanes (1.991%), Arthrospira (1.138%), Flavobacterium (0.857%), Sphingomonas (0.790%), Mycoplana (0.726%), and Pseudomonas (0.688%) were the dominant bacterial genera present in cooled soil. Key soil fungal communities, including Pseudaleuria (18.307%), Phoma (9.968%), Eocronartium (3.527%), Trichosporon (1.791%), and Pyrenochaeta (0.171%), were also recovered from cooled soil. The present results demonstrate that the growth of temperate crops is dependent on soil temperature, which subsequently affects the abundance and diversity of soil microbial communities that maintain the growth of temperate crops at low soil temperatures.
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Affiliation(s)
- Nurul Syazwani Ahmad Sabri
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia (UTM)Kuala LumpurMalaysia
| | - Zuriati Zakaria
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia (UTM)Kuala LumpurMalaysia
| | - Shaza Eva Mohamad
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia (UTM)Kuala LumpurMalaysia
| | - A Bakar Jaafar
- Ocean Thermal Energy Centre, Universiti Teknologi Malaysia (UTM)Kuala LumpurMalaysia
| | - Hirofumi Hara
- Department of Chemical Process Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia (UTM)Kuala LumpurMalaysia
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159
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Microbial Taxa and Soil Organic Carbon Accumulation Driven by Tree Roots. FORESTS 2018. [DOI: 10.3390/f9060333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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160
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De Porcellinis AJ, Nørgaard H, Brey LMF, Erstad SM, Jones PR, Heazlewood JL, Sakuragi Y. Overexpression of bifunctional fructose-1,6-bisphosphatase/sedoheptulose-1,7-bisphosphatase leads to enhanced photosynthesis and global reprogramming of carbon metabolism in Synechococcus sp. PCC 7002. Metab Eng 2018; 47:170-183. [PMID: 29510212 DOI: 10.1016/j.ymben.2018.03.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 02/02/2018] [Accepted: 03/01/2018] [Indexed: 12/25/2022]
Abstract
Cyanobacteria fix atmospheric CO2 to biomass and through metabolic engineering can also act as photosynthetic factories for sustainable productions of fuels and chemicals. The Calvin Benson cycle is the primary pathway for CO2 fixation in cyanobacteria, algae and C3 plants. Previous studies have overexpressed the Calvin Benson cycle enzymes, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and bifunctional sedoheptulose-1,7-bisphosphatase/fructose-1,6-bisphosphatase (hereafter BiBPase), in both plants and algae, although their impacts on cyanobacteria have not yet been rigorously studied. Here, we show that overexpression of BiBPase and RuBisCO have distinct impacts on carbon metabolism in the cyanobacterium Synechococcus sp. PCC 7002 through physiological, biochemical, and proteomic analyses. The former enhanced growth, cell size, and photosynthetic O2 evolution, and coordinately upregulated enzymes in the Calvin Benson cycle including RuBisCO and fructose-1,6-bisphosphate aldolase. At the same time it downregulated enzymes in respiratory carbon metabolism (glycolysis and the oxidative pentose phosphate pathway) including glucose-6-phosphate dehydrogenase (G6PDH). The content of glycogen was also significantly reduced while the soluble carbohydrate content increased. These results indicate that overexpression of BiBPase leads to global reprogramming of carbon metabolism in Synechococcus sp. PCC 7002, promoting photosynthetic carbon fixation and carbon partitioning towards non-storage carbohydrates. In contrast, whilst overexpression of RuBisCO had no measurable impact on growth and photosynthetic O2 evolution, it led to coordinated increase in the abundance of proteins involved in pyruvate metabolism and fatty acid biosynthesis. Our results underpin that singular genetic modifications in the Calvin Benson cycle can have far broader cellular impact than previously expected. These features could be exploited to more efficiently direct carbons towards desired bioproducts.
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Affiliation(s)
- Alice Jara De Porcellinis
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark; Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark; Carlsberg Research Laboratory, 100 Ny Carlsberg Vej, 1799 Copenhagen V, Denmark
| | - Hanne Nørgaard
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark; Novo Nordisk, Novo Nordisk Park 1, 2760 Måløv, Denmark
| | - Laura Maria Furelos Brey
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark; Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark
| | - Simon Matthé Erstad
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark; Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark
| | - Patrik R Jones
- Department Life Sciences, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, UK
| | - Joshua L Heazlewood
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Yumiko Sakuragi
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark; Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg DK-1871, Denmark.
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161
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Mógor ÁF, de Oliveira Amatussi J, Mógor G, Bocchetti de Lara G. Bioactivity of Cyanobacterial Biomass Related to Amino Acids Induces Growth and Metabolic Changes on Seedlings and Yield Gains of Organic Red Beet. ACTA ACUST UNITED AC 2018. [DOI: 10.4236/ajps.2018.95074] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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162
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Stephen AJ, Archer SA, Orozco RL, Macaskie LE. Advances and bottlenecks in microbial hydrogen production. Microb Biotechnol 2017; 10:1120-1127. [PMID: 28834420 PMCID: PMC5609275 DOI: 10.1111/1751-7915.12790] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 07/01/2017] [Indexed: 11/28/2022] Open
Abstract
Biological production of hydrogen is poised to become a significant player in the future energy mix. This review highlights recent advances and bottlenecks in various approaches to biohydrogen processes, often in concert with management of organic wastes or waste CO2. Some key bottlenecks are highlighted in terms of the overall energy balance of the process and highlighting the need for economic and environmental life cycle analyses with regard also to socio‐economic and geographical issues.
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Affiliation(s)
- Alan J Stephen
- School ofChemical Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Sophie A Archer
- School ofChemical Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Rafael L Orozco
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Lynne E Macaskie
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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163
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Building a bio-based industry in the Middle East through harnessing the potential of the Red Sea biodiversity. Appl Microbiol Biotechnol 2017; 101:4837-4851. [PMID: 28528426 PMCID: PMC5486811 DOI: 10.1007/s00253-017-8310-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 04/24/2017] [Accepted: 04/26/2017] [Indexed: 01/03/2023]
Abstract
The incentive for developing microbial cell factories for production of fuels and chemicals comes from the ability of microbes to deliver these valuable compounds at a reduced cost and with a smaller environmental impact compared to the analogous chemical synthesis. Another crucial advantage of microbes is their great biological diversity, which offers a much larger "catalog" of molecules than the one obtainable by chemical synthesis. Adaptation to different environments is one of the important drives behind microbial diversity. We argue that the Red Sea, which is a rather unique marine niche, represents a remarkable source of biodiversity that can be geared towards economical and sustainable bioproduction processes in the local area and can be competitive in the international bio-based economy. Recent bioprospecting studies, conducted by the King Abdullah University of Science and Technology, have established important leads on the Red Sea biological potential, with newly isolated strains of Bacilli and Cyanobacteria. We argue that these two groups of local organisms are currently most promising in terms of developing cell factories, due to their ability to operate in saline conditions, thus reducing the cost of desalination and sterilization. The ability of Cyanobacteria to perform photosynthesis can be fully exploited in this particular environment with one of the highest levels of irradiation on the planet. We highlight the importance of new experimental and in silico methodologies needed to overcome the hurdles of developing efficient cell factories from the Red Sea isolates.
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164
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Chellapandi P, Mohamed Khaja Hussain M, Prathiviraj R. CPSIR-CM: A database for structural properties of proteins identified in cyanobacterial C1 metabolism. ALGAL RES 2017. [DOI: 10.1016/j.algal.2016.12.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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165
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166
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Suthar H, Hingurao K, Vaghashiya J, Parmar J. Fermentation: A Process for Biofertilizer Production. MICROORGANISMS FOR SUSTAINABILITY 2017. [DOI: 10.1007/978-981-10-6241-4_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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167
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Singh JS, Koushal S, Kumar A, Vimal SR, Gupta VK. Book Review: Microbial Inoculants in Sustainable Agricultural Productivity- Vol. II: Functional Application. Front Microbiol 2016. [PMCID: PMC5179502 DOI: 10.3389/fmicb.2016.02105] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jay Shankar Singh
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar (Central) UniversityLucknow, India
- *Correspondence: Jay Shankar Singh
| | - Sumit Koushal
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar (Central) UniversityLucknow, India
| | - Arun Kumar
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar (Central) UniversityLucknow, India
| | - Shobhit R. Vimal
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar (Central) UniversityLucknow, India
| | - Vijai K. Gupta
- Molecular Glyco-biotechnology Group, Discipline of Biochemistry, School of Natural Sciences, National University of Ireland Galway (NUI)Galway, Ireland
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168
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Cassier-Chauvat C, Veaudor T, Chauvat F. Comparative Genomics of DNA Recombination and Repair in Cyanobacteria: Biotechnological Implications. Front Microbiol 2016; 7:1809. [PMID: 27881980 PMCID: PMC5101192 DOI: 10.3389/fmicb.2016.01809] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/27/2016] [Indexed: 12/16/2022] Open
Abstract
Cyanobacteria are fascinating photosynthetic prokaryotes that are regarded as the ancestors of the plant chloroplast; the purveyors of oxygen and biomass for the food chain; and promising cell factories for an environmentally friendly production of chemicals. In colonizing most waters and soils of our planet, cyanobacteria are inevitably challenged by environmental stresses that generate DNA damages. Furthermore, many strains engineered for biotechnological purposes can use DNA recombination to stop synthesizing the biotechnological product. Hence, it is important to study DNA recombination and repair in cyanobacteria for both basic and applied research. This review reports what is known in a few widely studied model cyanobacteria and what can be inferred by mining the sequenced genomes of morphologically and physiologically diverse strains. We show that cyanobacteria possess many E. coli-like DNA recombination and repair genes, and possibly other genes not yet identified. E. coli-homolog genes are unevenly distributed in cyanobacteria, in agreement with their wide genome diversity. Many genes are extremely well conserved in cyanobacteria (mutMS, radA, recA, recFO, recG, recN, ruvABC, ssb, and uvrABCD), even in small genomes, suggesting that they encode the core DNA repair process. In addition to these core genes, the marine Prochlorococcus and Synechococcus strains harbor recBCD (DNA recombination), umuCD (mutational DNA replication), as well as the key SOS genes lexA (regulation of the SOS system) and sulA (postponing of cell division until completion of DNA reparation). Hence, these strains could possess an E. coli-type SOS system. In contrast, several cyanobacteria endowed with larger genomes lack typical SOS genes. For examples, the two studied Gloeobacter strains lack alkB, lexA, and sulA; and Synechococcus PCC7942 has neither lexA nor recCD. Furthermore, the Synechocystis PCC6803 lexA product does not regulate DNA repair genes. Collectively, these findings indicate that not all cyanobacteria have an E. coli-type SOS system. Also interestingly, several cyanobacteria possess multiple copies of E. coli-like DNA repair genes, such as Acaryochloris marina MBIC11017 (2 alkB, 3 ogt, 7 recA, 3 recD, 2 ssb, 3 umuC, 4 umuD, and 8 xerC), Cyanothece ATCC51142 (2 lexA and 4 ruvC), and Nostoc PCC7120 (2 ssb and 3 xerC).
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Affiliation(s)
- Corinne Cassier-Chauvat
- Institute for Integrative Biology of the Cell, CEA, Centre Nationnal de la Recherche Scientifique (CNRS), Universite Paris-Sud, Université Paris-Saclay Gif-sur-Yvette Cedex, France
| | - Théo Veaudor
- Institute for Integrative Biology of the Cell, CEA, Centre Nationnal de la Recherche Scientifique (CNRS), Universite Paris-Sud, Université Paris-Saclay Gif-sur-Yvette Cedex, France
| | - Franck Chauvat
- Institute for Integrative Biology of the Cell, CEA, Centre Nationnal de la Recherche Scientifique (CNRS), Universite Paris-Sud, Université Paris-Saclay Gif-sur-Yvette Cedex, France
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Singh JS, Gupta VK. Degraded Land Restoration in Reinstating CH4 Sink. Front Microbiol 2016; 7:923. [PMID: 27379053 PMCID: PMC4905942 DOI: 10.3389/fmicb.2016.00923] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 05/31/2016] [Indexed: 11/13/2022] Open
Abstract
Methane (CH4), a potent greenhouse gas, contributes about one third to the global green house gas emissions. CH4-assimilating microbes (mostly methanotrophs) in upland soils play very crucial role in mitigating the CH4 release into the atmosphere. Agricultural, environmental, and climatic shifts can alter CH4 sink profiles of soils, likely through shifts in CH4-assimilating microbial community structure and function. Landuse change, as forest and grassland ecosystems altered to agro-ecosystems, has already attenuated the soil CH4 sink potential, and are expected to be continued in the future. We hypothesized that variations in CH4 uptake rates in soils under different landuse practices could be an indicative of alterations in the abundance and/or type of methanotrophic communities in such soils. However, only a few studies have addressed to number and methanotrophs diversity and their correlation with the CH4 sink potential in soils of rehabilitated/restored lands. We focus on landuse practices that can potentially mitigate CH4 gas emissions, the most prominent of which are improved cropland, grazing land management, use of bio-fertilizers, and restoration of degraded lands. In this perspective paper, it is proposed that restoration of degraded lands can contribute considerably to improved soil CH4 sink strength by retrieving/conserving abundance and assortment of efficient methanotrophic communities. We believe that this report can assist in identifying future experimental directions to the relationships between landuse changes, methane-assimilating microbial communities and soil CH4 sinks. The exploitation of microbial communities other than methanotrophs can contribute significantly to the global CH4 sink potential and can add value in mitigating the CH4 problems.
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Affiliation(s)
- Jay Shankar Singh
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar University Lucknow, India
| | - Vijai K Gupta
- Molecular Glyco-biotechnology Group, Discipline of Biochemistry, School of Natural Sciences, National University of Ireland Galway Galway, Ireland
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