1
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Du J, Li Y, Huang Y, Zhang D, Li L. Characterization of a novel monooxygenase originating from a deep-sea sediment metagenomic library. Appl Microbiol Biotechnol 2023; 107:6237-6249. [PMID: 37581624 DOI: 10.1007/s00253-023-12719-6] [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: 02/27/2023] [Revised: 07/12/2023] [Accepted: 08/01/2023] [Indexed: 08/16/2023]
Abstract
Oxygenases are important biocatalysts to produce many industrially important biomolecules. Here, a novel oxygenase, named MoxA, was identified through screening of a deep-sea sediment metagenomic library. Sequence analysis showed MoxA contains 424 amino acid residues with a predicated molecular mass of 46.9 kDa. Multiple sequence alignment and phylogenetic analysis indicated the sequence might be a new member of monooxygenase subfamily. A recombinant MoxA was obtained through the functional expression of moxA gene in Escherichia coli. Characterization of the purified MoxA indicated that it is an alkaline oxygenase showing maximal activity at pH 8.0. The optimal temperature of MoxA was 37 ℃, and it retained more than 70% of its initial activity after 1 h at 20-50 ℃ exhibiting good thermostability. Furthermore, effect of metal ions and organic solvents on enzymatic activity was investigated, and the results showed that the activity of MoxA was enhanced by Cu2+, Zn2+, Co2+ and Mg2+ at 1 mM, and by Co2+, Ca2+ and Mg2+ at 5 mM. Moreover, the recombinant strain harboring MoxA was used as a whole-cell biocatalyst for the efficient biosynthesis of indigo showing promising conversion efficiency. The biochemical properties of MoxA indicated that it would provide great contribution for the indigo bioproduction. KEY POINTS: • A novel monooxygenase from a metagenomic library was characterized. • The activity of MoxA was enhanced by metal ions at 1 mM and 5 mM. • MoxA has an optimal temperature of 37 ℃ and exhibited high conversion capacity.
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Affiliation(s)
- Jikun Du
- Central Research Laboratory, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, 518104, China.
| | - Yuanhua Li
- Central Research Laboratory, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, 518104, China
- Traditional Chinese Medicine and New Drug Research Institute, Department of Pharmacology, Guangdong Medical University, Dongguan, 523808, China
| | - Yali Huang
- College of Fundamental Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Dawei Zhang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Li Li
- Traditional Chinese Medicine and New Drug Research Institute, Department of Pharmacology, Guangdong Medical University, Dongguan, 523808, China.
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2
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Raiyani NM, Singh SP. Microbial community and predictive functionalities associated with the marine sediment of Coastal Gujarat. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:43245-43266. [PMID: 36650368 DOI: 10.1007/s11356-023-25196-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 01/04/2023] [Indexed: 01/19/2023]
Abstract
Marine sediments are complex ecosystems where structures and functions constantly change due to natural and anthropogenic influences. In this investigation, a comprehensive and comparative analysis of the bacterial communities and their functional potential of the pristine and polluted marine sediments were carried out using MiSeq. The phylum Proteobacteria was dominant in all study sites. Other phyla were Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Chloroflexi, Nitrospirae, Cyanobacteria, Verrucomicrobia, Tenericutes, and Chlorobi. Interestingly, about 50% of genera belong to the unclassified categories. The key genera were identified as Acinetobacter, Bacillus, Pseudomona, Idiomarina, Thalassospira, and Marinobacter, Halomonas, Planctomyces, Psychrobacter, and Vogesella. PICRUSt analysis revealed that major functions are associated with the metabolism category. Additionally, metabolism related to amino acids, carbohydrates, energy generation, xenobiotics degradation, nitrogen, sulfate, and methane were prominent. Similarly, the predicted metabolisms by COG and KEGG were observed in the microbial communities of the marine sediments. To date, a comprehensive description of the microbial life with metabolic potential in these study sites has not been investigated. This study therefore significantly adds to our understanding of the microbiome and its functional attributes of marine sediments.
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Affiliation(s)
- Nirali M Raiyani
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, 360 005, Gujarat, India
| | - Satya P Singh
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, 360 005, Gujarat, India.
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3
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Zhou Z, Meng H, Gu W, Li J, Deng M, Gu JD. High-throughput sequencing reveals the main drivers of niche-differentiation of bacterial community in the surface sediments of the northern South China sea. MARINE ENVIRONMENTAL RESEARCH 2022; 178:105641. [PMID: 35594805 DOI: 10.1016/j.marenvres.2022.105641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/28/2022] [Accepted: 04/30/2022] [Indexed: 05/16/2023]
Abstract
Studies on marine bacterial communities have revealed endemism in local communities, yet the underlying mechanisms remained elusive. Environmental gradient settings can benefit the straightaway study of community composition changes and the mechanisms explaining them. Here, MiSeq-based 16S rRNA gene sequencing was performed on 12 surface sediment samples from the northern South China Sea (nSCS) revealing that shallow-sea samples had a higher alpha diversity than deep-sea samples, and were differentiated from them significantly based on beta diversity. Temperature, seawater depth, and salinity were the top three influential factors. Bacterial 16S rRNA gene abundance was positively correlated with temperature, and negatively correlated with salinity. Sulfate-reducing bacteria including Desulfobacteraceae, Desulfobulbaceae, and Syntrophobacteraceae were enriched in shallow-sea sediments, co-abundant with nitrite-oxidizing Nitrospira and potential sulfur-oxidizing shallow-sea specific Woeseiaceae/JTB255 clade. Meanwhile, the co-existing and co-abundant of marine anammox and n-damo bacteria were enriched in deep-sea sediments, which was firstly evidenced in this study. The global deep-sea cosmopolitans, OM1 clade, and deep-sea specific Woeseiaceae/JTB255 clade were also found enriched in deep-sea sediments of nSCS. The discovery of novel taxa which were differentially enriched in shallow-/deep-sea sediments not only shed light on enigmatic physiological properties and the natural selection mechanism, but also provided the potential ecological-functional links which invoked further genomics-based metabolic characteristics.
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Affiliation(s)
- Zhichao Zhou
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Han Meng
- School of Environment, Nanjing Normal University, 122 Ninghai Road, Nanjing, Jiangsu, 210023, China
| | - Wenjie Gu
- Insitute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences/Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Guangdong Engineering Research Center of Soil Microbes and Cultivated Land Conservation, 66 Jinying Road, Guangzhou, Guangdong, 510640, China
| | - Jing Li
- Department of Food and Bioengineering, Guangdong Industry Polytechnic, Guangzhou, Guangdong, 510300, China
| | - Maocheng Deng
- Department of Food and Bioengineering, Guangdong Industry Polytechnic, Guangzhou, Guangdong, 510300, China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, China; Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, China.
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4
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Padhy SR, Bhattacharyya P, Dash PK, Nayak SK, Parida SP, Baig MJ, Mohapatra T. Elucidation of dominant energy metabolic pathways of methane, sulphur and nitrogen in respect to mangrove-degradation for climate change mitigation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 303:114151. [PMID: 34844054 DOI: 10.1016/j.jenvman.2021.114151] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/02/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
Mangroves play a key role in ecosystem balancing and climate change mitigation. It acts as a source and sink of methane (CH4), a major greenhouse gas responsible for climate change. Energy metabolic pathways of methane production (methanogenesis) and oxidation (methanotrophy) are directly driven by sulphur (S) and nitrogen (N) metabolism and salinity in coastal wetlands. To investigate, how mangrove-degradations, affect the source-sink behaviour of CH4; the pathways of CH4, S and N were studied through whole-genome metagenomic approach. Soil samples were collected from degraded and undisturbed mangrove systems in Sundarban, India. Structural and functional microbial diversities (KEGG pathways) of CH4, S and N metabolism were analysed and correlated with labile carbon pools and physico-chemical properties of soil. Overall, the acetoclastic pathway of methanogenesis was dominant. However, the relative proportion of conversion of CO2 to CH4 was more in degraded mangroves. Methane oxidation was higher in undisturbed mangroves and the serine pathway was dominant. After serine, the ribulose monophosphate pathway of CH4 oxidation was dominant in degraded mangrove, while the xylulose monophosphate pathway was dominant in undisturbed site as it is more tolerant to salinity and higher pH. The assimilatory pathway (AMP) of S-metabolism was dominant in both systems. But in AMP pathway, adenosine triphosphate sulfurylase enzyme reads were higher in degraded mangrove, while NADPH-sulfite reductase abundance was higher in undisturbed mangrove due to higher salinity, and pH. In N-metabolism, the denitrification pathway was predominant in degraded sites, whereas the dissimilatory nitrate reduction pathway was dominant in undisturbed mangroves. The relative ratios of sulphur reducing bacteria (SRB): methanogens were higher in degraded mangrove; however, methanotrophs:methanogens was higher in undisturbed mangrove indicated lower source and greater sink capacity of CH4 in the system. Microbial manipulation in mangrove-rhizosphere for regulating major energy metabolic pathways of methane could open-up a new window of climate change mitigation in coastal wetlands.
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Affiliation(s)
- S R Padhy
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India; Maharaja Sriram Chandra Bhanja Deo University, Baripada, Odisha, India.
| | - P Bhattacharyya
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India.
| | - P K Dash
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India.
| | - S K Nayak
- Maharaja Sriram Chandra Bhanja Deo University, Baripada, Odisha, India.
| | - S P Parida
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India.
| | - M J Baig
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India.
| | - T Mohapatra
- Indian Council of Agricultural Research, New Delhi, India.
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Zhang J, Zhang Y, Liu R, Cai R, Liu F, Sun C. Iocasia fonsfrigidae NS-1 gen. nov., sp. nov., a Novel Deep-Sea Bacterium Possessing Diverse Carbohydrate Metabolic Pathways. Front Microbiol 2021; 12:725159. [PMID: 34899621 PMCID: PMC8652127 DOI: 10.3389/fmicb.2021.725159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
Resolving metabolisms of deep-sea microorganisms is crucial for understanding ocean energy cycling. Here, a strictly anaerobic, Gram-negative strain NS-1 was isolated from the deep-sea cold seep in the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain NS-1 was most closely related to the type strain Halocella cellulosilytica DSM 7362T (with 92.52% similarity). A combination of phylogenetic, genomic, and physiological traits with strain NS-1, was proposed to be representative of a novel genus in the family Halanaerobiaceae, for which Iocasia fonsfrigidae NS-1 was named. It is noteworthy that I. fonsfrigidae NS-1 could metabolize multiple carbohydrates including xylan, alginate, starch, and lignin, and thereby produce diverse fermentation products such as hydrogen, lactate, butyrate, and ethanol. The expressions of the key genes responsible for carbohydrate degradation as well as the production of the above small molecular substrates when strain NS-1 cultured under different conditions, were further analyzed by transcriptomic methods. We thus predicted that part of the ecological role of Iocasia sp. is likely in the fermentation of products from the degradation of diverse carbohydrates to produce hydrogen as well as other small molecules, which are in turn utilized by other members of cold seep microbes.
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Affiliation(s)
- Jing Zhang
- CAS Key Laboratory of Experimental Marine Biology and Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Science, University of Chinese Academy of Sciences, Beijing, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,School of Life Sciences, Hebei University, Baoding, China
| | - Yuechao Zhang
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Rui Liu
- CAS Key Laboratory of Experimental Marine Biology and Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Ruining Cai
- CAS Key Laboratory of Experimental Marine Biology and Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Science, University of Chinese Academy of Sciences, Beijing, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Fanghua Liu
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Chaomin Sun
- CAS Key Laboratory of Experimental Marine Biology and Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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6
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Guo C, Zhang X, Luan S, Zhou H, Liu L, Qu Y. Diversity and structure of soil bacterial community in intertidal zone of Daliao River estuary, Northeast China. MARINE POLLUTION BULLETIN 2021; 163:111965. [PMID: 33450443 DOI: 10.1016/j.marpolbul.2020.111965] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Soil samples from the intertidal zone of Daliao River, Northeast China, were collected in three seasons (autumn, L1; winter, L2; and spring, L3) to evaluate the diversity and structure of bacterial community using high-throughput sequencing. Soil physicochemical characteristics varied greatly with seasons, and the potential nitrification rates were detected in the range of 1.04-2.71 μg NO3--N·g-1 dry soil·h-1 with the highest rate in spring (L3). Soil bacterial communities also differed seasonally, and nitrogen nutrients were the important variables affecting the bacterial communities as demonstrated by distance-based redundancy analysis and Mantel tests. Proteobacteria was the predominant phylum in soils showing a descending trend from L1 to L3. Woeseia and Ignatzschineria, both affiliating with Gammaproteobacteria, were the two most dominant genera, but they exerted different seasonal variations. The predicted functional profiles revealed 6 major nitrogen cycling processes, and the functional genes in relation to denitrification process were dominant in intertidal soils.
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Affiliation(s)
- Chaochen Guo
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China
| | - Xuwang Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China.
| | - Shimeng Luan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China
| | - Hao Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China
| | - Lifen Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China; Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
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7
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Zhang B, Li Y, Xiang SZ, Yan Y, Yang R, Lin MP, Wang XM, Xue YL, Guan XY. Sediment Microbial Communities and Their Potential Role as Environmental Pollution Indicators in Xuande Atoll, South China Sea. Front Microbiol 2020; 11:1011. [PMID: 32523570 PMCID: PMC7261833 DOI: 10.3389/fmicb.2020.01011] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 04/24/2020] [Indexed: 11/13/2022] Open
Abstract
In this study, 39 sediment samples were collected from Qilian Island, Iltis Bank, and Yongxing Island in Xuande Atoll in the South China Sea (SCS), and the microbial community structures and distribution were analyzed. The microbial community was influenced by both natural environmental factors and human activities. The abundance of genera Vibrio and Pseudoalteromonas, which are associated with pathogenicity and pollutant degradation, were significantly higher in Qilian Island than in Yongxing Island and Iltis Bank, suggesting possible contamination of Qilian Island area through human activities. Pathogenic or typical pollutants-degrading bacteria were found to be negatively correlated with most of the commonly occurring bacterial populations in marine sediment, and these bacteria were more likely to appear in the sediment of deep water layer. This co-occurrence pattern may be due to bacterial adaptation to environmental changes such as depth and contaminations from human activities, including garbage disposal, farming, and oil spills from ships. The findings of this study could help in understanding the potential influences of human activities on the ecosystem at the microbial level.
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Affiliation(s)
- Biao Zhang
- School of Ocean Sciences, China University of Geosciences, Beijing, China
| | - Yan Li
- School of Ocean Sciences, China University of Geosciences, Beijing, China
| | - Shi-Zheng Xiang
- School of Ocean Sciences, China University of Geosciences, Beijing, China
| | - Yu Yan
- School of Ocean Sciences, China University of Geosciences, Beijing, China
| | - Rui Yang
- School of Ocean Sciences, China University of Geosciences, Beijing, China
| | - Meng-Ping Lin
- School of Ocean Sciences, China University of Geosciences, Beijing, China
| | - Xue-Mu Wang
- Marine Geological Survey Institute of Hainan Province, Haikou, China
| | - Yu-Long Xue
- Marine Geological Survey Institute of Hainan Province, Haikou, China
| | - Xiang-Yu Guan
- School of Ocean Sciences, China University of Geosciences, Beijing, China.,Hebei Marine Resource Survey Center, Qinhuangdao, China
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8
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Microbial production of cyanophycin: From enzymes to biopolymers. Biotechnol Adv 2019; 37:107400. [PMID: 31095967 DOI: 10.1016/j.biotechadv.2019.05.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/30/2019] [Accepted: 05/11/2019] [Indexed: 11/20/2022]
Abstract
Cyanophycin is an attractive biopolymer with chemical and material properties that are suitable for industrial applications in the fields of food, medicine, cosmetics, nutrition, and agriculture. For efficient production of cyanophycin, considerable efforts have been exerted to characterize cyanophycin synthetases (CphAs) and optimize fermentations and downstream processes. In this paper, we review the characteristics of diverse CphAs from cyanobacteria and non-cyanobacteria. Furthermore, strategies for cyanophycin production in microbial strains, including Escherichia coli, Pseudomonas putida, Ralstonia eutropha, Rhizopus oryzae, and Saccharomyces cerevisiae, heterologously expressing different cphA genes are reviewed. Additionally, chemical and material properties of cyanophycin and its derivatives produced through biological or chemical modifications are reviewed in the context of their industrial applications. Finally, future perspectives on microbial production of cyanophycin are provided to improve its cost-effectiveness.
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9
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Su Z, Dai T, Tang Y, Tao Y, Huang B, Mu Q, Wen D. Sediment bacterial community structures and their predicted functions implied the impacts from natural processes and anthropogenic activities in coastal area. MARINE POLLUTION BULLETIN 2018; 131:481-495. [PMID: 29886974 DOI: 10.1016/j.marpolbul.2018.04.052] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 04/20/2018] [Accepted: 04/20/2018] [Indexed: 06/08/2023]
Abstract
Coastal ecosystem structures and functions are changing under natural and anthropogenic influences. In this study, surface sediment samples were collected from disturbed zone (DZ), near estuary zone (NEZ), and far estuary zone (FEZ) of Hangzhou Bay, one of the most seriously polluted bays in China. The bacterial community structures and predicted functions varied significantly in different zones. Firmicutes were found most abundantly in DZ, highlighting the impacts of anthropogenic activities. Sediment total phosphorus was most influential on the bacterial community structures. Predicted by PICRUSt analysis, DZ significantly exceeded FEZ and NEZ in the subcategory of Xenobiotics Biodegradation and Metabolism; and DZ enriched all the nitrate reduction related genes, except nrfA gene. Seawater salinity and inorganic nitrogen, respectively as the representative natural and anthropogenic factor, performed exact-oppositely in nitrogen metabolism functions. The changes of bacterial community compositions and predicted functions provide a new insight into human-induced pollution impacts on coastal ecosystem.
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Affiliation(s)
- Zhiguo Su
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Tianjiao Dai
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yushi Tang
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yile Tao
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Bei Huang
- Zhejiang Provincial Zhoushan Marine Ecological Environmental Monitoring Station, Zhoushan 316021, China
| | - Qinglin Mu
- Zhejiang Provincial Zhoushan Marine Ecological Environmental Monitoring Station, Zhoushan 316021, China
| | - Donghui Wen
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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10
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Patel V, Munot H, Shah V, Shouche YS, Madamwar D. Taxonomic profiling of bacterial community structure from coastal sediment of Alang-Sosiya shipbreaking yard near Bhavnagar, India. MARINE POLLUTION BULLETIN 2015; 101:736-745. [PMID: 26475023 DOI: 10.1016/j.marpolbul.2015.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/14/2015] [Accepted: 10/04/2015] [Indexed: 06/05/2023]
Abstract
The Alang-Sosiya shipbreaking yard (ASSBY) is considered the largest of its kind in the world, and a major source of anthropogenic pollutants. The aim of this study was to investigate the impact of shipbreaking activities on the bacterial community structure with a combination of culture-dependent and culture-independent approaches. In the culture-dependent approach, 200 bacterial cultures were isolated and analyzed by molecular fingerprinting and 16S ribosomal RNA (r-RNA) gene sequencing, as well as being studied for degradation of polycyclic aromatic hydrocarbons (PAHs). In the culture-independent approach, operational taxonomic units (OTUs) were related to eight major phyla, of which Betaproteobacteria (especially Acidovorax) was predominantly found in the polluted sediments of ASSBY and Gammaproteobacteria in the pristine sediment sample. The statistical approaches showed a significant difference in the bacterial community structure between the pristine and polluted sediments. To the best of our knowledge, this is the first study investigating the effect of shipbreaking activity on the bacterial community structure of the coastal sediment at ASSBY.
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Affiliation(s)
- Vilas Patel
- Environmental Genomics and Proteomics Lab, BRD School of Biosciences, Vadtal Road, Satellite Campus, Post Box No. 39, Sardar Patel University, Vallabh Vidyanagar 388 120, Anand, Gujarat, India.
| | - Hitendra Munot
- Molecular Biology Unit, National Center for Cell Science, Ganeshkhind, Pune 411 007, Maharashtra, India
| | - Varun Shah
- Environmental Genomics and Proteomics Lab, BRD School of Biosciences, Vadtal Road, Satellite Campus, Post Box No. 39, Sardar Patel University, Vallabh Vidyanagar 388 120, Anand, Gujarat, India
| | - Yogesh S Shouche
- Molecular Biology Unit, National Center for Cell Science, Ganeshkhind, Pune 411 007, Maharashtra, India
| | - Datta Madamwar
- Environmental Genomics and Proteomics Lab, BRD School of Biosciences, Vadtal Road, Satellite Campus, Post Box No. 39, Sardar Patel University, Vallabh Vidyanagar 388 120, Anand, Gujarat, India.
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11
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Metaproteomic analysis of bacterial communities in marine mudflat aquaculture sediment. World J Microbiol Biotechnol 2015; 31:1397-408. [DOI: 10.1007/s11274-015-1891-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/12/2015] [Indexed: 10/23/2022]
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12
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Du J, Xiao K, Li L, Ding X, Liu H, Lu Y, Zhou S. Temporal and spatial diversity of bacterial communities in coastal waters of the South china sea. PLoS One 2013; 8:e66968. [PMID: 23785512 PMCID: PMC3681761 DOI: 10.1371/journal.pone.0066968] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 05/14/2013] [Indexed: 01/09/2023] Open
Abstract
Bacteria are recognized as important drivers of biogeochemical processes in all aquatic ecosystems. Temporal and geographical patterns in ocean bacterial communities have been observed in many studies, but the temporal and spatial patterns in the bacterial communities from the South China Sea remained unexplored. To determine the spatiotemporal patterns, we generated 16S rRNA datasets for 15 samples collected from the five regularly distributed sites of the South China Sea in three seasons (spring, summer, winter). A total of 491 representative sequences were analyzed by MOTHUR, yielding 282 operational taxonomic units (OTUs) grouped at 97% stringency. Significant temporal variations of bacterial diversity were observed. Richness and diversity indices indicated that summer samples were the most diverse. The main bacterial group in spring and summer samples was Alphaproteobacteria, followed by Cyanobacteria and Gammaproteobacteria, whereas Cyanobacteria dominated the winter samples. Spatial patterns in the samples were observed that samples collected from the coastal (D151, D221) waters and offshore (D157, D1512, D224) waters clustered separately, the coastal samples harbored more diverse bacterial communities. However, the temporal pattern of the coastal site D151 was contrary to that of the coastal site D221. The LIBSHUFF statistics revealed noticeable differences among the spring, summer and winter libraries collected at five sites. The UPGMA tree showed there were temporal and spatial heterogeneity of bacterial community composition in coastal waters of the South China Sea. The water salinity (P=0.001) contributed significantly to the bacteria-environment relationship. Our results revealed that bacterial community structures were influenced by environmental factors and community-level changes in 16S-based diversity were better explained by spatial patterns than by temporal patterns.
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Affiliation(s)
- Jikun Du
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Department of Clinical Laboratory, Shenzhen Shajing Affiliated Hospital of Guangzhou Medical University, Shenzhen, China
| | - Kai Xiao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Li Li
- Department of Pharmacology, Guangdong Medical College, Dongguan, China
- * E-mail: (LL); (SZ)
| | - Xian Ding
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Helu Liu
- Department of Clinical Laboratory, Shenzhen Shajing Affiliated Hospital of Guangzhou Medical University, Shenzhen, China
| | - Yongjun Lu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shining Zhou
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- * E-mail: (LL); (SZ)
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Du J, Li L, Ding X, Hu H, Lu Y, Zhou S. Isolation and characterization of a novel cyanophycin synthetase from a deep-sea sediment metagenomic library. Appl Microbiol Biotechnol 2013; 97:8619-28. [DOI: 10.1007/s00253-013-4872-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Revised: 03/18/2013] [Accepted: 03/20/2013] [Indexed: 10/27/2022]
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