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Annunziata R, Mele BH, Marotta P, Volpe M, Entrambasaguas L, Mager S, Stec K, d’Alcalà MR, Sanges R, Finazzi G, Iudicone D, Montresor M, Ferrante MI. Trade-off between sex and growth in diatoms: Molecular mechanisms and demographic implications. SCIENCE ADVANCES 2022; 8:eabj9466. [PMID: 35044817 PMCID: PMC8769554 DOI: 10.1126/sciadv.abj9466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Diatoms are fast-growing and winning competitors in aquatic environments, possibly due to optimized growth performance. However, their life cycles are complex, heteromorphic, and not fully understood. Here, we report on the fine control of cell growth and physiology during the sexual phase of the marine diatom Pseudo-nitzschia multistriata. We found that mating, under nutrient replete conditions, induces a prolonged growth arrest in parental cells. Transcriptomic analyses revealed down-regulation of genes related to major metabolic functions from the early phases of mating. Single-cell photophysiology also pinpointed an inhibition of photosynthesis and storage lipids accumulated in the arrested population, especially in gametes and zygotes. Numerical simulations revealed that growth arrest affects the balance between parental cells and their siblings, possibly favoring the new generation. Thus, in addition to resources availability, life cycle traits contribute to shaping the species ecological niches and must be considered to describe and understand the structure of plankton communities.
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Affiliation(s)
- Rossella Annunziata
- Stazione Zoologica Anton Dohrn, Napoli, Italy
- Corresponding author. (R.A.); (M.I.F.)
| | | | | | | | | | | | | | | | - Remo Sanges
- International School for Advanced Studies (SISSA), Via Bonomea 265, Trieste 34136, Italy
| | - Giovanni Finazzi
- Université Grenoble Alpes (UGA), Centre National Recherche Scientifique (CNRS), Commissariat Energie Atomique, Energies Alternatives (CEA), Institut National Recherche Agriculture, Alimentation, Environnement (INRAE), Interdisciplinary Research Institute of Grenoble, IRIG-Laboratoire de Physiologie Cellulaire et Végétale, Grenoble, France
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2
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Liu G, Vijayaraman SB, Dong Y, Li X, Andongmaa BT, Zhao L, Tu J, He J, Lin L. Bacillus velezensis LG37: transcriptome profiling and functional verification of GlnK and MnrA in ammonia assimilation. BMC Genomics 2020; 21:215. [PMID: 32143571 PMCID: PMC7060608 DOI: 10.1186/s12864-020-6621-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 02/25/2020] [Indexed: 11/14/2022] Open
Abstract
Background In recent years, interest in Bacillus velezensis has increased significantly due to its role in many industrial water bioremediation processes. In this study, we isolated and assessed the transcriptome of Bacillus velezensis LG37 (from an aquaculture pond) under different nitrogen sources. Since Bacillus species exhibit heterogeneity, it is worth investigating the molecular mechanism of LG37 through ammonia nitrogen assimilation, where nitrogen in the form of molecular ammonia is considered toxic to aquatic organisms. Results Here, a total of 812 differentially expressed genes (DEGs) from the transcriptomic sequencing of LG37 grown in minimal medium supplemented with ammonia (treatment) or glutamine (control) were obtained, from which 56 had Fold Change ≥2. BLAST-NCBI and UniProt databases revealed 27 out of the 56 DEGs were potentially involved in NH4+ assimilation. Among them, 8 DEGs together with the two-component regulatory system GlnK/GlnL were randomly selected for validation by quantitative real-time RT-PCR, and the results showed that expression of all the 8 DEGs are consistent with the RNA-seq data. Moreover, the transcriptome and relative expression analysis were consistent with the transporter gene amtB and it is not involved in ammonia transport, even in the highest ammonia concentrations. Besides, CRISPR-Cas9 knockout and overexpression glnK mutants further evidenced the exclusion of amtB regulation, suggesting the involvement of alternative transporter. Additionally, in the transcriptomic data, a novel ammonium transporter mnrA was expressed significantly in increased ammonia concentrations. Subsequently, OEmnrA and ΔmnrA LG37 strains showed unique expression pattern of specific genes compared to that of wild-LG37 strain. Conclusion Based on the transcriptome data, regulation of nitrogen related genes was determined in the newly isolated LG37 strain to analyse the key regulating factors during ammonia assimilation. Using genomics tools, the novel MnrA transporter of LG37 became apparent in ammonia transport instead of AmtB, which transports ammonium nitrogen in other Bacillus strains. Collectively, this study defines heterogeneity of B. velezensis LG37 through comprehensive transcriptome analysis and subsequently, by genome editing techniques, sheds light on the enigmatic mechanisms controlling the functional genes under different nitrogen sources also reveals the need for further research.
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Affiliation(s)
- Guangxin Liu
- State Key Laboratory of Agricultural Microbiology, College of Fisheries and College of Life Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.,Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Sarath Babu Vijayaraman
- Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Yanjun Dong
- State Key Laboratory of Agricultural Microbiology, College of Fisheries and College of Life Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Xinfeng Li
- State Key Laboratory of Agricultural Microbiology, College of Fisheries and College of Life Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Binda Tembeng Andongmaa
- State Key Laboratory of Agricultural Microbiology, College of Fisheries and College of Life Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Lijuan Zhao
- Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Jiagang Tu
- State Key Laboratory of Agricultural Microbiology, College of Fisheries and College of Life Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
| | - Jin He
- State Key Laboratory of Agricultural Microbiology, College of Fisheries and College of Life Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China.
| | - Li Lin
- State Key Laboratory of Agricultural Microbiology, College of Fisheries and College of Life Sciences, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China. .,Guangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology, Qingdao, 266071, Shandong, China.
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3
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Bodénès P, Wang HY, Lee TH, Chen HY, Wang CY. Microfluidic techniques for enhancing biofuel and biorefinery industry based on microalgae. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:33. [PMID: 30815031 PMCID: PMC6376642 DOI: 10.1186/s13068-019-1369-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/03/2019] [Indexed: 05/03/2023]
Abstract
This review presents a critical assessment of emerging microfluidic technologies for the application on biological productions of biofuels and other chemicals from microalgae. Comparisons of cell culture designs for the screening of microalgae strains and growth conditions are provided with three categories: mechanical traps, droplets, or microchambers. Emerging technologies for the in situ characterization of microalgae features and metabolites are also presented and evaluated. Biomass and secondary metabolite productivities obtained at microscale are compared with the values obtained at bulk scale to assess the feasibility of optimizing large-scale operations using microfluidic platforms. The recent studies in microsystems for microalgae pretreatment, fractionation and extraction of metabolites are also reviewed. Finally, comments toward future developments (high-pressure/-temperature process; solvent-resistant devices; omics analysis, including genome/epigenome, proteome, and metabolome; biofilm reactors) of microfluidic techniques for microalgae applications are provided.
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Affiliation(s)
- Pierre Bodénès
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Hsiang-Yu Wang
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, Taiwan
- Institute of Nuclear Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Tsung-Hua Lee
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Hung-Yu Chen
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Chun-Yen Wang
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, Taiwan
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4
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Yung MMN, Fougères PA, Leung YH, Liu F, Djurišić AB, Giesy JP, Leung KMY. Physicochemical characteristics and toxicity of surface-modified zinc oxide nanoparticles to freshwater and marine microalgae. Sci Rep 2017; 7:15909. [PMID: 29162907 PMCID: PMC5698420 DOI: 10.1038/s41598-017-15988-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/02/2017] [Indexed: 01/25/2023] Open
Abstract
Because of wide applications of surface-modified zinc oxide nanoparticles (ZnO-NPs) in commercial sunscreens and their easiness of being released into water, concerns have been raised over their potential effects on aquatic organisms. This study compared physicochemical properties of silane-coated and uncoated ZnO-NPs to elucidate their toxic potencies toward three freshwater and three marine microalgae. Surfaces of ZnO-NPs (20 nm) were modified by coating with 3-aminopropyltrimethoxysilane (A-ZnO-NPs) that provides the particles with a more hydrophilic surface, or dodecyltrichlorosilane (D-ZnO-NPs) that turns the particles to hydrophobic. Uncoated ZnO-NPs formed larger aggregates and released more Zn2+ than did either of the two coated ZnO-NPs. The three nanoparticles formed larger aggregates but released less Zn2+ at pH 8 than at pH 7. Although sensitivities varied among algal species, A-ZnO-NPs and uncoated ZnO-NPs were more potent at inhibiting growth of algal cells than were D-ZnO-NPs after 96-h exposure to ZnO, uncoated ZnO-NPs, each of the coated ZnO-NPs or ZnSO4 at 10 concentrations ranging from 0.1 to 100 mg/L. The marine diatom Thalassiosira pseudonana exposed to ZnO-NPs, A-ZnO-NPs or D-ZnO-NPs resulted in differential expressions of genes, suggesting that each of the coatings resulted in ZnO-NPs acting through different mechanisms of toxic action.
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Affiliation(s)
- Mana M N Yung
- The Swire Institute of Marine Science and School of Biological Sciences, the University of Hong Kong, Pokfulam, Hong Kong, China
| | - Paul-Antoine Fougères
- The Swire Institute of Marine Science and School of Biological Sciences, the University of Hong Kong, Pokfulam, Hong Kong, China.,Université de Bordeaux, Bordeaux, France
| | - Yu Hang Leung
- Department of Physics, the University of Hong Kong, Pokfulam, Hong Kong, China
| | - Fangzhou Liu
- Department of Physics, the University of Hong Kong, Pokfulam, Hong Kong, China
| | | | - John P Giesy
- The Swire Institute of Marine Science and School of Biological Sciences, the University of Hong Kong, Pokfulam, Hong Kong, China.,Department of Veterinary Biomedical Sciences and Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.,State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Kenneth M Y Leung
- The Swire Institute of Marine Science and School of Biological Sciences, the University of Hong Kong, Pokfulam, Hong Kong, China. .,State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China.
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5
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Chen Z, Chen L, Zhang W. Tools for Genomic and Transcriptomic Analysis of Microbes at Single-Cell Level. Front Microbiol 2017; 8:1831. [PMID: 28979258 PMCID: PMC5611438 DOI: 10.3389/fmicb.2017.01831] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 09/06/2017] [Indexed: 12/16/2022] Open
Abstract
Microbiologists traditionally study population rather than individual cells, as it is generally assumed that the status of individual cells will be similar to that observed in the population. However, the recent studies have shown that the individual behavior of each single cell could be quite different from that of the whole population, suggesting the importance of extending traditional microbiology studies to single-cell level. With recent technological advances, such as flow cytometry, next-generation sequencing (NGS), and microspectroscopy, single-cell microbiology has greatly enhanced the understanding of individuality and heterogeneity of microbes in many biological systems. Notably, the application of multiple ‘omics’ in single-cell analysis has shed light on how individual cells perceive, respond, and adapt to the environment, how heterogeneity arises under external stress and finally determines the fate of the whole population, and how microbes survive under natural conditions. As single-cell analysis involves no axenic cultivation of target microorganism, it has also been demonstrated as a valuable tool for dissecting the microbial ‘dark matter.’ In this review, current state-of-the-art tools and methods for genomic and transcriptomic analysis of microbes at single-cell level were critically summarized, including single-cell isolation methods and experimental strategies of single-cell analysis with NGS. In addition, perspectives on the future trends of technology development in the field of single-cell analysis was also presented.
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Affiliation(s)
- Zixi Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin UniversityTianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin UniversityTianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin UniversityTianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China.,Center for Biosafety Research and Strategy, Tianjin UniversityTianjin, China
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6
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Jian J, Zeng D, Wei W, Lin H, Li P, Liu W. The Combination of RNA and Protein Profiling Reveals the Response to Nitrogen Depletion in Thalassiosira pseudonana. Sci Rep 2017; 7:8989. [PMID: 28827639 PMCID: PMC5566445 DOI: 10.1038/s41598-017-09546-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 07/24/2017] [Indexed: 12/21/2022] Open
Abstract
Nitrogen (N) is essential for the growth of algae, and its concentration varies greatly in the ocean, which has been regarded as a limitation for phytoplankton growth. Despite its great importance, most of the existing studies on the mechanisms underlying the effects of N on diatoms have focused on physiology, biochemistry and a few target genes and have rarely involved whole genomic analyses. Therefore, in this study, we integrated physiological data with RNA and protein profiling data to reveal the response strategy of Thalassiosira pseudonana under N-depleted conditions. Physiological measurements indicated that the cell growth capacity and chlorophyll content of the cells decreased, as did the expression of photosynthesis- and chlorophyll biosynthesis-related genes or proteins. The RNA-Seq profile results showed that T. pseudonana responded to N deprivation through increases in glycolysis, the TCA cycle and N metabolism as well as down-regulation in the Calvin cycle, gluconeogenesis, pentose phosphate, oxidative phosphorylation and lipid synthesis. These results provide a basic understanding for further research addressing how N affects phytoplankton in terms of genomics.
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Affiliation(s)
- Jianbo Jian
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Dezhi Zeng
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Wei Wei
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Hongmin Lin
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Ping Li
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China.
| | - Wenhua Liu
- Marine Biology Institute, Shantou University, Shantou, Guangdong, 515063, P.R. China.
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7
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Zhang Q, Wang T, Zhou Q, Zhang P, Gong Y, Gou H, Xu J, Ma B. Development of a facile droplet-based single-cell isolation platform for cultivation and genomic analysis in microorganisms. Sci Rep 2017; 7:41192. [PMID: 28112223 PMCID: PMC5253770 DOI: 10.1038/srep41192] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 12/15/2016] [Indexed: 12/19/2022] Open
Abstract
Wider application of single-cell analysis has been limited by the lack of an easy-to-use and low-cost strategy for single-cell isolation that can be directly coupled to single-cell sequencing and single-cell cultivation, especially for small-size microbes. Herein, a facile droplet microfluidic platform was developed to dispense individual microbial cells into conventional standard containers for downstream analysis. Functional parts for cell encapsulation, droplet inspection and sorting, as well as a chip-to-tube capillary interface were integrated on one single chip with simple architecture, and control of the droplet sorting was achieved by a low-cost solenoid microvalve. Using microalgal and yeast cells as models, single-cell isolation success rate of over 90% and single-cell cultivation success rate of 80% were demonstrated. We further showed that the individual cells isolated can be used in high-quality DNA and RNA analyses at both gene-specific and whole-genome levels (i.e. real-time quantitative PCR and genome sequencing). The simplicity and reliability of the method should improve accessibility of single-cell analysis and facilitate its wider application in microbiology researches.
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Affiliation(s)
- Qiang Zhang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Tingting Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Qian Zhou
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.,Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Peng Zhang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Yanhai Gong
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Honglei Gou
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Bo Ma
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
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8
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Wang J, Chen L, Chen Z, Zhang W. RNA-seq based transcriptomic analysis of single bacterial cells. Integr Biol (Camb) 2016; 7:1466-76. [PMID: 26331465 DOI: 10.1039/c5ib00191a] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Gene-expression heterogeneity among individual cells determines the fate of a bacterial population. Here we report the first bacterial single-cell RNA sequencing (RNA-seq), BaSiC RNA-seq, a method integrating RNA isolation, cDNA synthesis and amplification, and RNA-seq analysis of the whole transcriptome of single cyanobacterium Synechocystis sp. PCC 6803 cells which typically contain approximately 5-7 femtogram total RNA per cell. We applied the method to 3 Synechocystis single cells at 24 h and 3 single cells at 72 h after nitrogen-starvation stress treatment, as well as their bulk-cell controls under the same conditions, to determine the heterogeneity upon environmental stress. With 82-98% and 31-48% of all putative Synechocystis genes identified in single cells of 24 and 72 h, respectively, the results demonstrated that the method could achieve good identification of the transcripts in single bacterial cells. In addition, the preliminary results from nitrogen-starved cells also showed a possible increasing gene-expression heterogeneity from 24 h to 72 h after nitrogen starvation stress. Moreover, preliminary analysis of single-cell transcriptomic datasets revealed that genes from the "Mobile elements" functional category have the most significant increase of gene-expression heterogeneity upon stress, which was further confirmed by single-cell RT-qPCR analysis of gene expression in 24 randomly selected cells.
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Affiliation(s)
- Jiangxin Wang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P. R. China. and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, P. R. China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P. R. China. and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, P. R. China
| | - Zixi Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P. R. China. and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, P. R. China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P. R. China. and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, P. R. China
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9
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Qi Z, Chen L, Zhang W. Comparison of Transcriptional Heterogeneity of Eight Genes between Batch Desulfovibrio vulgaris Biofilm and Planktonic Culture at a Single-Cell Level. Front Microbiol 2016; 7:597. [PMID: 27199927 PMCID: PMC4847118 DOI: 10.3389/fmicb.2016.00597] [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: 07/22/2015] [Accepted: 04/11/2016] [Indexed: 11/13/2022] Open
Abstract
Sulfate-reducing bacteria (SRB) biofilm formed on metal surfaces can change the physicochemical properties of metals and cause metal corrosion. To enhance understanding of differential gene expression in Desulfovibrio vulgaris under planktonic and biofilm growth modes, a single-cell based RT-qPCR approach was applied to determine gene expression levels of 8 selected target genes in four sets of the 31 individual cells isolated from each growth condition (i.e., biofilm formed on a mild steel (SS) and planktonic cultures, exponential and stationary phases). The results showed obvious gene-expression heterogeneity for the target genes among D. vulgaris single cells of both biofilm and planktonic cultures. In addition, an increased gene-expression heterogeneity in the D. vulgaris biofilm when compared with the planktonic culture was also observed for seven out of eight selected genes at exponential phase, and six out of eight selected genes at stationary phase, respectively, which may be contributing to the increased complexity in terms of structures and morphology in the biofilm. Moreover, the results showed up-regulation of DVU0281 gene encoding exopolysaccharide biosynthesis protein, and down-regulation of genes involved in energy metabolism (i.e., DVU0434 and DVU0588), stress responses (i.e., DVU2410) and response regulator (i.e., DVU3062) in the D. vulgaris biofilm cells. Finally, the gene (DVU2571) involved in iron transportation was found down-regulated, and two genes (DVU1340 and DVU1397) involved in ferric uptake repressor and iron storage were up-regulated in D. vulgaris biofilm, suggesting their possible roles in maintaining normal metabolism of the D. vulgaris biofilm under environments of high concentration of iron. This study showed that the single-cell based analysis could be a useful approach in deciphering metabolism of microbial biofilms.
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Affiliation(s)
- Zhenhua Qi
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin UniversityTianjin, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin UniversityTianjin, China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin UniversityTianjin, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin UniversityTianjin, China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin UniversityTianjin, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin UniversityTianjin, China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
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10
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Piccinetti CC, Ricci R, Pennesi C, Radaelli G, Totti C, Norici A, Giordano M, Olivotto I. Herbivory in the soft coral Sinularia flexibilis (Alcyoniidae). Sci Rep 2016; 6:22679. [PMID: 26951778 PMCID: PMC4782107 DOI: 10.1038/srep22679] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/17/2016] [Indexed: 11/09/2022] Open
Abstract
Our work provides strong support for the hypothesis that Sinularia flexibilis ingests diatoms such as Thalassiosira pseudonana. We assessed algal ingestion by S. flexibilis through estimates of algal removal, histological analyses, scanning electron microscopy observations, and gene expression determination (18S and silicon transporter 1) by real time PCR. Cell counts are strongly suggestive of algal removal by the coral; light and scanning microscopy provide qualitative evidence for the ingestion of T. pseudonana by S. flexibilis, while molecular markers did not prove to be sufficiently selective/specific to give clear results. We thus propose that previous instances of inability of corals to ingest algae are reconsidered using different technical approach, before concluding that coral herbivory is not a general feature.
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Affiliation(s)
- Chiara C Piccinetti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Roberta Ricci
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Chiara Pennesi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Giuseppe Radaelli
- Dipartimento di Biomedicina Comparata e Alimentazione, Università degli Studi di Padova, Agripolis, Viale dell'Università, 16, 35020 Legnaro, Italy
| | - Cecilia Totti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Alessandra Norici
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Mario Giordano
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.,Institute of Microbiology ASCR, Centrum Algatech, Laboratory of photosynthesis, Opatovický mlýn, 379 81 Třeboň, Czech Republic.,National Research Council, Institute of Marine Science, Venezia, Italy
| | - Ike Olivotto
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
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Shi X, Chen CH, Gao W, Chao SH, Meldrum DR. Parallel RNA extraction using magnetic beads and a droplet array. LAB ON A CHIP 2015; 15:1059-65. [PMID: 25519439 PMCID: PMC4349128 DOI: 10.1039/c4lc01111b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Nucleic acid extraction is a necessary step for most genomic/transcriptomic analyses, but it often requires complicated mechanisms to be integrated into a lab-on-a-chip device. Here, we present a simple, effective configuration for rapidly obtaining purified RNA from low concentration cell medium. This Total RNA Extraction Droplet Array (TREDA) utilizes an array of surface-adhering droplets to facilitate the transportation of magnetic purification beads seamlessly through individual buffer solutions without solid structures. The fabrication of TREDA chips is rapid and does not require a microfabrication facility or expertise. The process takes less than 5 minutes. When purifying mRNA from bulk marine diatom samples, its repeatability and extraction efficiency are comparable to conventional tube-based operations. We demonstrate that TREDA can extract the total mRNA of about 10 marine diatom cells, indicating that the sensitivity of TREDA approaches single-digit cell numbers.
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Affiliation(s)
- Xu Shi
- Center for Biosignatures Discovery Automation , The Biodesign Institute , Arizona State University Tempe , Arizona , USA .
| | - Chun-Hong Chen
- Center for Biosignatures Discovery Automation , The Biodesign Institute , Arizona State University Tempe , Arizona , USA .
- Department of Electrical Engineering , National Cheng Kung University Tainan , Taiwan
| | - Weimin Gao
- Center for Biosignatures Discovery Automation , The Biodesign Institute , Arizona State University Tempe , Arizona , USA .
| | - Shih-hui Chao
- Center for Biosignatures Discovery Automation , The Biodesign Institute , Arizona State University Tempe , Arizona , USA .
| | - Deirdre R. Meldrum
- Center for Biosignatures Discovery Automation , The Biodesign Institute , Arizona State University Tempe , Arizona , USA .
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12
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Single-cell analysis reveals gene-expression heterogeneity in syntrophic dual-culture of Desulfovibrio vulgaris with Methanosarcina barkeri. Sci Rep 2014; 4:7478. [PMID: 25504148 PMCID: PMC4265775 DOI: 10.1038/srep07478] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 11/25/2014] [Indexed: 01/09/2023] Open
Abstract
Microbial syntrophic metabolism has been well accepted as the heart of how methanogenic and other anaerobic microbial communities function. In this work, we applied a single-cell RT-qPCR approach to reveal gene-expression heterogeneity in a model syntrophic system of Desulfovibrio vulgaris and Methanosarcina barkeri, as compared with the D. vulgaris monoculture. Using the optimized primers and single-cell analytical protocol, we quantitatively determine gene-expression levels of 6 selected target genes in each of the 120 single cells of D. vulgaris isolated from its monoculture and dual-culture with M. barkeri. The results demonstrated very significant cell-to-cell gene-expression heterogeneity for the selected D. vulgaris genes in both the monoculture and the syntrophic dual-culture. Interestingly, no obvious increase in gene-expression heterogeneity for the selected genes was observed for the syntrophic dual-culture when compared with its monoculture, although the community structure and cell-cell interactions have become more complicated in the syntrophic dual-culture. In addition, the single-cell RT-qPCR analysis also provided further evidence that the gene cluster (DVU0148-DVU0150) may be involved syntrophic metabolism between D. vulgaris and M. barkeri. Finally, the study validated that single-cell RT-qPCR analysis could be a valuable tool in deciphering gene functions and metabolism in mixed-cultured microbial communities.
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Palenik B. Molecular mechanisms by which marine phytoplankton respond to their dynamic chemical environment. ANNUAL REVIEW OF MARINE SCIENCE 2014; 7:325-340. [PMID: 25195866 DOI: 10.1146/annurev-marine-010814-015639] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Marine scientists have long been interested in the interactions of marine phytoplankton with their chemical environments. Nutrient availability clearly controls carbon fixation on a global scale, but the interactions between phytoplankton and nutrients are complex and include both short-term responses (seconds to minutes) and longer-term evolutionary adaptations. This review outlines how genomics and functional genomics approaches are providing a better understanding of these complex interactions, especially for cyanobacteria and diatoms, for which the genome sequences of multiple model organisms are available. Transporters and related genes are emerging as the most likely candidates for biomarkers in stress-specific studies, but other genes are also possible candidates. One surprise has been the important role of horizontal gene transfer in mediating chemical-biological interactions.
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Affiliation(s)
- Brian Palenik
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093-0202;
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Shi X, Gao W, Wang J, Chao SH, Zhang W, Meldrum DR. Measuring gene expression in single bacterial cells: recent advances in methods and micro-devices. Crit Rev Biotechnol 2014; 35:448-60. [DOI: 10.3109/07388551.2014.899556] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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