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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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Lu Y, Lv Y, Zhang Y, Liu Q, Xu X, Xiao X, Xu J. Metatranscriptomes reveal the diverse responses of Thaumarchaeota ecotypes to environmental variations in the northern slope of the South China Sea. Environ Microbiol 2023; 25:410-427. [PMID: 36448268 DOI: 10.1111/1462-2920.16289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022]
Abstract
Thaumarchaeota are among the most abundant prokaryotes in the ocean, playing important roles in carbon and nitrogen cycling. Marine Thaumarchaeota ecotypes exhibit depth-related diversification and seasonal changes. However, transcriptomic activities concerning niche partitioning among thaumarchaeal ecotypes remain unclear. Here, we examined the variations in the distribution and transcriptomic activity of marine Thaumarchaeota ecotypes. Three primary ecotypes were identified: a Nitrosopumilus-like clade; a Nitrosopelagicus-like water column A (WCA) clade, thriving in epipelagic water; and a water column B (WCB) clade, dominant in deep water. Depth-related partitioning of the three ecotypes and the seasonal variability of the WCA and WCB ecotypes were observed. Nutrient concentrations, chlorophyll α and salinity were the primary environmental factors. The relative abundance of the WCA ecotype and its transcript abundance of amoA gene were positively correlated with chlorophyll α and salinity, while the WCB ecotype was positively correlated with nitrate and phosphate. Based on high-quality metagenome-assembled genomes, transcriptomic analysis revealed that the three ecotypes exhibited various co-occurring expression patterns of the elemental cycling genes in the nitrogen, carbon, phosphorus, and sulfur cycles. Our results provide transcriptomic evidence of the niche differentiation of marine Thaumarchaeota ecotypes, highlighting the diverse roles of ecotypes and WCA subclades in biogeochemical cycles.
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Affiliation(s)
- Ye Lu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Yongxin Lv
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Liu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Xuewei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
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3
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Heterogeneous selection dominated the temporal variation of the planktonic prokaryotic community during different seasons in the coastal waters of Bohai Bay. Sci Rep 2022; 12:20475. [PMID: 36443487 PMCID: PMC9705714 DOI: 10.1038/s41598-022-24892-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
To explore temporal and spatial effects on the planktonic prokaryotic community composition (PCC) in the coastal region of the Bohai Sea, surface water samples were collected from 12 to 28 regularly distributed sites in Bohai Bay across 3 months from different seasons to characterize the PCC using high-throughput sequencing of the 16S rRNA V4 region. Prokaryotic α- and β-diversity showed significant temporal variation during the three sampling months. VPA analysis based on both weighted and unweighted UniFrac distances exhibited a shift of environmental and spatial effects on PCC variation with temporal variation. Quantification analysis of assembly processes on community turn over showed that "heterogeneous selection" dominated for PCC temporal variation, with basic abiotic parameters such as temperature, pH, ammonia nitrogen as the driving factors. Analysis of seasonal features showed that seasonal specific OTUs (ssOTUs) exhibited different seasonal attributions under the same phylum; meanwhile, the ssOTUs showed significant correlations with the driving environmental factors, which suggested that finer-level analysis was needed to more strictly reflect the temporal variation. Moreover, predicted nitrogen and sulfur metabolism were significantly shifted during the temporal variation. Our results clearly showed that seasonally varied environmental factors drive the "heterogeneous selection" process for PCC assembly in seawaters of Bohai Bay during different sampling seasons.
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Garlapati D, Kumar BC, Muthukumar C, Madeswaran P, Ramu K, Murthy MVR. Assessing the in situ bacterial diversity and composition at anthropogenically active sites using the environmental DNA (eDNA). MARINE POLLUTION BULLETIN 2021; 170:112593. [PMID: 34126444 DOI: 10.1016/j.marpolbul.2021.112593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 05/28/2021] [Accepted: 05/30/2021] [Indexed: 06/12/2023]
Abstract
In this study, we identified the in situ bacterial groups and their community structure in coastal waters influenced by anthropogenic inputs. The use of environmental DNA (eDNA) and high throughput sequencing (HTS) were employed to derive accurate and reliable information on bacterial abundance. The V3 and V4 hypervariable regions of the 16S rRNA gene were amplified and the sequences were clustered into operational taxonomic units to analyze the site-specific variations in community composition. The percentage composition within the bacterial orders varied significantly among nearshore anthropogenic hotspots and offshore (5 km) samples. The microbial network constructed taking the bacterial abundance as nodes displayed strong positive and negative correlations within the bacterial families. Overall, the use of eDNA coupled with HTS is an incredible means for monitoring and assessing the abundance of bacterial communities and also serves as a biomonitoring tool to understand the degree of anthropogenic contamination in coastal waters.
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Affiliation(s)
- Deviram Garlapati
- National Centre for Coastal Research, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, India.
| | - B Charan Kumar
- National Centre for Coastal Research, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, India
| | - C Muthukumar
- National Centre for Coastal Research, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, India
| | - P Madeswaran
- National Centre for Coastal Research, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, India
| | - K Ramu
- National Centre for Coastal Research, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, India
| | - M V Ramana Murthy
- National Centre for Coastal Research, Ministry of Earth Sciences (MoES), Government of India, Chennai 600100, India
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Lv J, Yuan R, Wang S. Water diversion induces more changes in bacterial and archaeal communities of river sediments than seasonality. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 293:112876. [PMID: 34098351 DOI: 10.1016/j.jenvman.2021.112876] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/01/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Previous studies have demonstrated that seasonal variation is often the most important factor affecting aquatic bacterial assemblages. Whether anthropogenic activities can dominate community dynamics remains unknown. Based on 16S rRNA high-throughput sequencing technology, this study revealed and compared the relative influence of water diversions and seasonality on bacterial and archaeal communities in river sediments from a region with obvious seasonality. The results indicate that the influence of water diversion on bacteria and archaea in water-receiving river sediments exceeded the influence of seasonal variation. Water diversion affected microbes by increasing EC, salinity, water flow rate, and organic matter carbon and nitrogen contents. Seasonal variations affected microbes by altering water temperature. Diversion responders but no season responders were classified by statistical methods in the microbial community. Diversion responder numbers were related to nitrogen concentrations, complex organic carbon contents and EC values, which were mainly affected by water diversion. With the joint impact of water diversion and seasonality, the correlations of bacterial and archaeal numbers with environmental factors were obviously weakened due to the increases in the ecological niche breadths of microorganisms. Natural seasonal changes in bacterial and archaeal communities were totally altered by changes in salinity, nutrients, and hydrological conditions induced by anthropogenic water diversions. These results highlight that human activity may be a stronger driver than natural seasonality in the alteration of bacterial and archaeal communities.
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Affiliation(s)
- Jiali Lv
- College of Environmental and Resource Sciences, Shanxi University, Taiyuan, 030006, China; Shanxi Laboratory for Yellow River, Taiyuan, 030006, China; Key Laboratory of Agricultural Water Resources Research, Innovation Academy for Seed Design, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China; Sino-Danish College of University of Chinese Academy of Sciences, Beijing, 101408, China; Sino-Danish Centre for Education and Research, Beijing, 101408, China
| | - Ruiqiang Yuan
- College of Environmental and Resource Sciences, Shanxi University, Taiyuan, 030006, China; Shanxi Laboratory for Yellow River, Taiyuan, 030006, China.
| | - Shiqin Wang
- Key Laboratory of Agricultural Water Resources Research, Innovation Academy for Seed Design, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
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6
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Bai S, Hou G. Microbial communities on fish eggs from Acanthopagrus schlegelii and Halichoeres nigrescens at the XuWen coral reef in the Gulf of Tonkin. PeerJ 2020; 8:e8517. [PMID: 32071819 PMCID: PMC7008816 DOI: 10.7717/peerj.8517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/05/2020] [Indexed: 01/21/2023] Open
Abstract
Coral reefs are an important part of the ocean ecosystem and are a vital spawning ground for marine fish. Microorganisms are abundant in this environment and play a key role in the growth and development of host species. Many studies have investigated the microbial communities of fish with a focus on the intestinal microbiome of laboratory-reared adult fish. Little is known about the relationship between fish eggs and their microorganisms, especially as microbial communities relate to wild fish eggs in coral reefs. In this study, we analyzed the microbial communities of two species of coral fish eggs, Acanthopagrus schlegelii and Halichoeres nigrescens, using 16S rRNA gene amplicon sequencing technology. Pseudomonas, Archromobacter, and Serratia were the main bacterial genera associated with these fish eggs and are known to be bacteria with potentially pathogenic and spoilage effects. The microbial community structures of Acanthopagrus schlegelii and Halichoeres nigrescens eggs were separated based on the 30 most abundant operational taxonomic units (OTUs). Principal coordinate analysis (PCoA) and non-metric multidimensional scaling analysis (NMDS) further confirmed that the microbial communities of coral fish eggs differ by species, which may be due to host selection. A functional prediction of the microbial communities indicated that most of the microbial communities were chemoheterotrophic and involved in nitrogen cycling. Our results showed that the microbial communities of coral fish eggs were distinct by species and that key microorganisms were potentially pathogenic, leading to the spoilage of fish eggs, high mortality, and low incubation rates. This study provided new insights for understanding the relationship between microorganisms and wild fish eggs.
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Affiliation(s)
- Shijie Bai
- Deep Sea Science Division, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Gang Hou
- Guangdong Ocean University, Zhanjiang, Guangdong, China
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7
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Zhao W, Wang J, Xu S, Lei Y, Yang R, Shi L, Wang X, Huang Z. Bacterioplankton community variation in Bohai Bay (China) is explained by joint effects of environmental and spatial factors. Microbiologyopen 2020; 9:e997. [PMID: 32022464 PMCID: PMC7142376 DOI: 10.1002/mbo3.997] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/23/2019] [Accepted: 12/31/2019] [Indexed: 02/01/2023] Open
Abstract
Parsing the relative importance of environmental (recent disturbances) and spatial factors (historical processes) in determining community structure is a core issue in ecology. The Bohai Bay is a typical semi‐enclosed bay located in the north of China, surrounding by the metropolitan area with anthropogenic disturbances made it a complex marine coastal system with pollution gradients, where the distributions and determinants of bacterioplankton communities remain unclear. In this study, we collected surface water samples from 19 sites across Bohai Bay at about 100 km scale to investigate the relative roles of local environments and regional spatial factors in shaping bacterioplankton community composition (BCC). The environmental parameters in the sampling region showed gradient change according to the geographic variation. Several abundant OTUs were significantly correlated with the pollution parameters in the studied area, and 16 OTUs of them showed distinct distribution pattern in different polluted regions with obvious geographic segmentation, which indicated the effects of pollution gradient and dispersal limitation on specific taxon. The BCCs did not show obviously clustering effect between different polluted regions, which indicated the complexity for explaining the BCC variation in the studied region. The partial Mantel test revealed stronger spatial effects on beta diversity than those of local environmental factors, which indicated that dispersal limitation accounted more for the beta diversity than environmental heterogeneity. Furthermore, variation partitioning analysis (VPA) conducted by combining the environmental variables, linear trends, and principal coordinates of the variables from neighbor matrices (PCNM) showed that it was the joint effects of environmental and spatial factors contributed to the explained variation of BCC in the studied area. Considering the special human geography characteristics of Bohai Bay, the unmeasured biotic/abiotic factors, stochastic factors, and anthropogenic disturbances may be responsible for the unexplained variation of the BCC.
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Affiliation(s)
- Wei Zhao
- Tianjin Key Laboratory of Industrial Biological Systems and Process Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jingjing Wang
- Tianjin Key Laboratory of Industrial Biological Systems and Process Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Song Xu
- Tianjin Key Laboratory of Industrial Biological Systems and Process Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yu Lei
- Core Facility, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Rong Yang
- Tianjin Key Laboratory of Industrial Biological Systems and Process Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Liuyang Shi
- Tianjin Key Laboratory of Industrial Biological Systems and Process Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xingbiao Wang
- Tianjin Key Laboratory of Industrial Biological Systems and Process Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zhiyong Huang
- Tianjin Key Laboratory of Industrial Biological Systems and Process Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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Eduardo-Correia B, Morales-Filloy H, Abad JP. Bacteria From the Multi-Contaminated Tinto River Estuary (SW, Spain) Show High Multi-Resistance to Antibiotics and Point to Paenibacillus spp. as Antibiotic-Resistance-Dissemination Players. Front Microbiol 2020; 10:3071. [PMID: 31998281 PMCID: PMC6965355 DOI: 10.3389/fmicb.2019.03071] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 12/19/2019] [Indexed: 12/31/2022] Open
Abstract
Bacterial resistance to antibiotics is an ever-increasing phenomenon that, besides clinical settings, is generally assumed to be prevalent in environmental soils and waters. The analysis of bacteria resistant to each one of 11 antibiotics in waters and sediments of the Huelva’s estuary, a multi-contaminated environment, showed high levels of bacteria resistant mainly to Tm, among others. To further gain knowledge on the fate of multi-drug resistance (MDR) in environmental bacteria, 579 ampicillin-resistant bacteria were isolated tested for resistance to 10 antibiotics. 92.7% of the isolates were resistant to four or more antibiotic classes, indicating a high level of multi-resistance. 143 resistance profiles were found. The isolates with different MDR profiles and/or colony morphologies were phylogenetically ascribed based on 16S rDNA to phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, including 48 genera. Putative intrinsic resistance was detected in different phylogenetic groups including genera Altererythrobacter, Bacillus, Brevundimonas, Erythrobacter, Mesonia, Ochrobactrum, and Ponticaulis. Correlation of the presence of pairs of the non-intrinsic-resistances in phylogenetic groups based on the kappa index (κ) highlighted the co-habitation of some of the tested pairs at different phylogenetic levels. Maximum correlation (κ = 1.000) was found for pairs CzR/TcR in Betaproteobacteria, and CcR/TcR and EmR/SmR in Sphingobacteriia at the class level, while at the genus level, was found for CcR/TcR and NxR/TmR in Mesonia, CzR/TmR and EmR/KmR in Paenibacillus, and CcR/EmR and RpR/TcR in Pseudomonas. These results could suggest the existence of intra-class and intra-genus-transmissible genetic elements containing determinants for both members of each pair. Network analysis based on κ values higher than 0.4 indicated the sharing of paired resistances among several genera, many of them centered on the Paenibacillus node and raising the hypothesis of inter-genera transmission of resistances interconnected through members of this genus. This is the first time that a possible hotspot of resistance interchange in a particular environment may have been detected, opening up the possibility that one, or a few, bacterial members of the community could be important promoters of antibiotic resistance (AR) dissemination in this environment’s bacterial population. Further studies using the available isolates will likely give insights of the possible mechanisms and genetic elements involved.
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Affiliation(s)
- Benedito Eduardo-Correia
- Department of Molecular Biology, Faculty of Sciences-Biology Building, Universidad Autónoma de Madrid, Madrid, Spain
| | - Héctor Morales-Filloy
- Department of Molecular Biology, Faculty of Sciences-Biology Building, Universidad Autónoma de Madrid, Madrid, Spain
| | - José P Abad
- Department of Molecular Biology, Faculty of Sciences-Biology Building, Universidad Autónoma de Madrid, Madrid, Spain
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9
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He H, Fu L, Liu Q, Fu L, Bi N, Yang Z, Zhen Y. Community Structure, Abundance and Potential Functions of Bacteria and Archaea in the Sansha Yongle Blue Hole, Xisha, South China Sea. Front Microbiol 2019; 10:2404. [PMID: 31681249 PMCID: PMC6813542 DOI: 10.3389/fmicb.2019.02404] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/04/2019] [Indexed: 01/05/2023] Open
Abstract
The Sansha Yongle Blue Hole is the deepest blue hole in the world and exhibits unique environmental characteristics. In this paper, Illumina sequencing and qPCR analysis were conducted to obtain the microbial information in this special ecosystem. The results showed that the richness and diversity of bacterial communities in the hole was greater than those of archaeal communities, and bacterial and archaeal communities were dominated by Proteobacteria and Euryarchaeota, respectively. Temperature and nitrate concentration significantly contributed to the heterogeneous distribution of major bacterial clades; salinity explained most variations of the archaeal communities, but not significant. A sudden increase of bacterial 16S rRNA, archaeal 16S rRNA, ANAMMOX 16S rRNA, nirS and dsrB gene was noticed from 90 to 100 m in the hole probably due to more phytoplankton at this depth. Sulfur oxidation and nitrate reduction were the most abundant predicted ecological functions in the hole, while lots of archaea were predicted to be involved in aerobic ammonia oxidation and methanogenesis. The co-occurrence network analysis illustrated that a synergistic effect between sulfate reduction and sulfur oxidation, and between nitrogen fixation and denitrification, a certain degree of coupling between sulfur and nitrogen cycle was also observed in the hole. The comparisons of bacterial and archaeal communities between the hole and other caves in the world (or other areas of the South China Sea) suggest that similar conditions are hypothesized to give rise to similar microbial communities, and environmental conditions may contribute significantly to the bacterial and archaeal communities.
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Affiliation(s)
- Hui He
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lulu Fu
- Laboratory for Marine Ecology and Environmental Science, National Laboratory for Marine Science and Technology, Qingdao, China
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Qian Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China
| | - Liang Fu
- Sansha Trackline Institute of Coral Reef Environment Protection, Sansha, China
| | - Naishuang Bi
- College of Marine Geosciences, Ocean University of China, Qingdao, China
| | - Zuosheng Yang
- College of Marine Geosciences, Ocean University of China, Qingdao, China
| | - Yu Zhen
- Laboratory for Marine Ecology and Environmental Science, National Laboratory for Marine Science and Technology, Qingdao, China
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
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10
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Abundance and community composition of bacterioplankton in the Northern South China Sea during winter: geographic position and water layer influences. Biologia (Bratisl) 2018. [DOI: 10.2478/s11756-018-0023-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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11
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Hornick KM, Buschmann AH. Insights into the diversity and metabolic function of bacterial communities in sediments from Chilean salmon aquaculture sites. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-017-1317-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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12
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Distribution, Community Composition, and Potential Metabolic Activity of Bacterioplankton in an Urbanized Mediterranean Sea Coastal Zone. Appl Environ Microbiol 2017; 83:AEM.00494-17. [PMID: 28667110 DOI: 10.1128/aem.00494-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/20/2017] [Indexed: 12/15/2022] Open
Abstract
Bacterioplankton are fundamental components of marine ecosystems and influence the entire biosphere by contributing to the global biogeochemical cycles of key elements. Yet, there is a significant gap in knowledge about their diversity and specific activities, as well as environmental factors that shape their community composition and function. Here, the distribution and diversity of surface bacterioplankton along the coastline of the Gulf of Naples (GON; Italy) were investigated using flow cytometry coupled with high-throughput sequencing of the 16S rRNA gene. Heterotrophic bacteria numerically dominated the bacterioplankton and comprised mainly Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes Distinct communities occupied river-influenced, coastal, and offshore sites, as indicated by Bray-Curtis dissimilarity, distance metric (UniFrac), linear discriminant analysis effect size (LEfSe), and multivariate analyses. The heterogeneity in diversity and community composition was mainly due to salinity and changes in environmental conditions across sites, as defined by nutrient and chlorophyll a concentrations. Bacterioplankton communities were composed of a few dominant taxa and a large proportion (92%) of rare taxa (here defined as operational taxonomic units [OTUs] accounting for <0.1% of the total sequence abundance), the majority of which were unique to each site. The relationship between 16S rRNA and the 16S rRNA gene, i.e., between potential metabolic activity and abundance, was positive for the whole community. However, analysis of individual OTUs revealed high rRNA-to-rRNA gene ratios for most (71.6% ± 16.7%) of the rare taxa, suggesting that these low-abundance organisms were potentially active and hence might be playing an important role in ecosystem diversity and functioning in the GON.IMPORTANCE The study of bacterioplankton in coastal zones is of critical importance, considering that these areas are highly productive and anthropogenically impacted. Their richness and evenness, as well as their potential activity, are very important to assess ecosystem health and functioning. Here, we investigated bacterial distribution, community composition, and potential metabolic activity in the GON, which is an ideal test site due to its heterogeneous environment characterized by a complex hydrodynamics and terrestrial inputs of varied quantities and quality. Our study demonstrates that bacterioplankton communities in this region are highly diverse and strongly regulated by a combination of different environmental factors leading to their heterogeneous distribution, with the rare taxa contributing to a major proportion of diversity and shifts in community composition and potentially holding a key role in ecosystem functioning.
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13
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Experimental evaluation of the metabolic reversibility of ANME-2d between anaerobic methane oxidation and methanogenesis. Appl Microbiol Biotechnol 2016; 100:6481-6490. [DOI: 10.1007/s00253-016-7475-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 03/13/2016] [Accepted: 03/15/2016] [Indexed: 01/26/2023]
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14
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Sun FL, Wang YS, Wu ML, Sun CC, Cheng H. Spatial and vertical distribution of bacterial community in the northern South China Sea. ECOTOXICOLOGY (LONDON, ENGLAND) 2015; 24:1478-1485. [PMID: 25956981 DOI: 10.1007/s10646-015-1472-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/28/2015] [Indexed: 06/04/2023]
Abstract
Microbial communities are highly diverse in coastal oceans and response rapidly with changing environments. Learning about this will help us understand the ecology of microbial populations in marine ecosystems. This study aimed to assess the spatial and vertical distributions of the bacterial community in the northern South China Sea. Multi-dimensional scaling analyses revealed structural differences of the bacterial community among sampling sites and vertical depth. Result also indicated that bacterial community in most sites had higher diversity in 0-75 m depths than those in 100-200 m depths. Bacterial community of samples was positively correlation with salinity and depth, whereas was negatively correlation with temperature. Proteobacteria and Cyanobacteria were the dominant groups, which accounted for the majority of sequences. The α-Proteobacteria was highly diverse, and sequences belonged to Rhodobacterales bacteria were dominant in all characterized sequences. The current data indicate that the Rhodobacterales bacteria, especially Roseobacter clade are the diverse group in the tropical waters.
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Affiliation(s)
- Fu-Lin Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shenzhen, 518121, China
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shenzhen, 518121, China.
| | - Mei-Lin Wu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Cui-Ci Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Daya Bay Marine Biology Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shenzhen, 518121, China
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
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15
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New primers for detecting and quantifying denitrifying anaerobic methane oxidation archaea in different ecological niches. Appl Microbiol Biotechnol 2015; 99:9805-12. [PMID: 26300291 DOI: 10.1007/s00253-015-6893-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 07/28/2015] [Indexed: 10/23/2022]
Abstract
The significance of ANME-2d in methane sink in the environment has been overlooked, and there was no any study evaluating the distribution of ANME-2d in the environment. New primers were thus needed to be designed for following research. In this paper, a pair of primers (DP397F and DP569R) was designed to quantify ANME-2d. The specificity and amplification efficiency of this primer pair were acceptable. PCR amplification of another pair of primers (DP142F and DP779R) generated a single, bright targeted band from the enrichment sample, but yielded faint, multiple bands from the environmental samples. Nested PCR was conducted using the primers DP142F/DP779R in the first round and DP142F/DP569R in the second round, which generated a bright targeted band. Further phylogenetic analysis showed that these targeted bands were ANME-2d-related sequences. Real-time PCR showed that the copies of the 16s ribosomal RNA gene of ANME-2d in these samples ranged from 3.72 × 10(4) to 2.30 × 10(5) copies μg(-1) DNA, indicating that the percentage of ANME-2d was greatest in a polluted river sample and least in a rice paddy sample. These results demonstrate that the newly developed real-time PCR primers could sufficiently quantify ANME-2d and that nested PCR with an appropriate combination of the new primers could successfully detect ANME-2d in environmental samples; the latter finding suggests that ANME-2d may spread in environments.
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16
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Shan D, Wei G, Li M, Wang W, Li X, Gao Z, Shao Z. Distribution and diversity of bacterioplankton communities in subtropical seawater around Xiamen Island, China. Microbiol Res 2015; 175:16-23. [PMID: 25794799 DOI: 10.1016/j.micres.2015.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/01/2015] [Accepted: 02/07/2015] [Indexed: 01/28/2023]
Abstract
Marine bacterioplankton communities have profound impact on global biogeochemical cycles and ecological balances. However, relatively little is known about the bacterioplankton communities and the factors shaping their spatial distribution in subtropical island. Here, the bacterioplankton communities around a typical subtropical island, Xiamen Island, were revealed by analyzing bacterial 16S rRNA gene through quantitative PCR (qPCR) and 454 pyrosequencing methods. The qPCR results indicated that the abundance of 16S rRNA gene ranged from 2.07 × 10(7) to 2.13 × 10(8)copies mL(-1) in surface seawater among eight sampling sites (S1-S8) around Xiamen Island, and the nitrogen and phosphorus-rich sites (S5 and S8) were detected with higher 16S rRNA gene abundance. Pyrosequencing evidenced that a total of 267 genera of 47 classes in 26 different phyla (or candidate phyla) and some unclassified bacteria were obtained from seawater around Xiamen Island. The most dominant phylum was Proteobacteria (49.62-76.84% among sites), followed by Bacteroidetes (6.64-20.88%), Actinobacteria (2.58-9.20%), Firmicutes (0.03-13.30%), Verrucomicrobia (0.23-2.67%) and Planctomycetes (0.14-2.20%). Among eight sites, the nitrogen and phosphorus-rich sites (S5 and S8) exhibited higher proportions of Gammaproteobacteria, Epsilonproteobacteria, Firmicutes and lower proportions of Alphaproteobacteria and Planctomycetes than other sites. S5 and S8 also had more similar β-diversity, and sampling site near the estuary (S8) showed the highest bacterial diversity. Redundancy analysis (RDA) confirmed that total nitrogen and total phosphorus significantly (P<0.05 and P<0.01, respectively) influenced the bacterioplankton communities around Xiamen Island. These results will provide insights into bacterial abundance, diversity and distribution patterns, as well as their controlling factors, in subtropical marine ecosystems.
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Affiliation(s)
- Dapeng Shan
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, People's Republic of China
| | - Guangshan Wei
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, Shandong, People's Republic of China
| | - Mingcong Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, Shandong, People's Republic of China
| | - Wanpeng Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, People's Republic of China
| | - Xu Li
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, People's Republic of China
| | - Zheng Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, Shandong, People's Republic of China.
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, People's Republic of China.
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17
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Foong CP, Lau NS, Deguchi S, Toyofuku T, Taylor TD, Sudesh K, Matsui M. Whole genome amplification approach reveals novel polyhydroxyalkanoate synthases (PhaCs) from Japan Trench and Nankai Trough seawater. BMC Microbiol 2014; 14:318. [PMID: 25539583 PMCID: PMC4326521 DOI: 10.1186/s12866-014-0318-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 12/10/2014] [Indexed: 11/16/2022] Open
Abstract
Background Special features of the Japanese ocean include its ranges of latitude and depth. This study is the first to examine the diversity of Class I and II PHA synthases (PhaC) in DNA samples from pelagic seawater taken from the Japan Trench and Nankai Trough from a range of depths from 24 m to 5373 m. PhaC is the key enzyme in microorganisms that determines the types of monomer units that are polymerized into polyhydroxyalkanoate (PHA) and thus affects the physicochemical properties of this thermoplastic polymer. Complete putative PhaC sequences were determined via genome walking, and the activities of newly discovered PhaCs were evaluated in a heterologous host. Results A total of 76 putative phaC PCR fragments were amplified from the whole genome amplified seawater DNA. Of these 55 clones contained conserved PhaC domains and were classified into 20 genetic groups depending on their sequence similarity. Eleven genetic groups have undisclosed PhaC activity based on their distinct phylogenetic lineages from known PHA producers. Three complete DNA coding sequences were determined by IAN-PCR, and one PhaC was able to produce poly(3-hydroxybutyrate) in recombinant Cupriavidus necator PHBˉ4 (PHB-negative mutant). Conclusions A new functional PhaC that has close identity to Marinobacter sp. was discovered in this study. Phylogenetic classification for all the phaC genes isolated from uncultured bacteria has revealed that seawater and other environmental resources harbor a great diversity of PhaCs with activities that have not yet been investigated. Functional evaluation of these in silico-based PhaCs via genome walking has provided new insights into the polymerizing ability of these enzymes. Electronic supplementary material The online version of this article (doi:10.1186/s12866-014-0318-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Choon Pin Foong
- Synthetic Genomics Research Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan. .,Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia.
| | - Nyok-Sean Lau
- Synthetic Genomics Research Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan. .,Centre for Chemical Biology, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia.
| | - Shigeru Deguchi
- R&D Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.
| | - Takashi Toyofuku
- R&D Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.
| | - Todd D Taylor
- Laboratory for Integrated Bioinformatics, Core for Precise Measuring and Modeling, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, 230-0045, Japan.
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia. .,Centre for Chemical Biology, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia.
| | - Minami Matsui
- Synthetic Genomics Research Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan.
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18
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Patel V, Munot H, Shouche YS, Madamwar D. Response of bacterial community structure to seasonal fluctuation and anthropogenic pollution on coastal water of Alang-Sosiya ship breaking yard, Bhavnagar, India. BIORESOURCE TECHNOLOGY 2014; 161:362-370. [PMID: 24727696 DOI: 10.1016/j.biortech.2014.03.033] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 02/26/2014] [Accepted: 03/04/2014] [Indexed: 06/03/2023]
Abstract
Bacterial community structure was analyzed from coastal water of Alang-Sosiya ship breaking yard (ASSBY), world's largest ship breaking yard, near Bhavnagar, using 16S rRNA gene sequencing (cultured dependent and culture independent). In clone libraries, total 2324 clones were retrieved from seven samples (coastal water of ASSBY for three seasons along with one pristine coastal water) which were grouped in 525 operational taxonomic units. Proteobacteria was found to be dominant in all samples. In pristine samples, Gammaproteobacteria was found to be dominant, whereas in polluted samples dominancy of Gammaproteobacteria has shifted to Betaproteobacteria and Epsilonproteobacteria. Richness and diversity indices also indicated that bacterial community in pristine sample was the most diverse followed by summer, monsoon and winter samples. To the best of knowledge, this is the first study describing bacterial community structure from coastal water of ASSBY, and it suggests that seasonal fluctuation and anthropogenic pollutions alters the bacterial community structure.
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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, Gujarat, India.
| | - Hitendra Munot
- Molecular Biology Unit, National Center for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India
| | - Yogesh S Shouche
- Molecular Biology Unit, National Center for Cell Science, Ganeshkhind, Pune 411007, 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, Gujarat, India.
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