1
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Zahra SA, Persiani R, Dueholm MK, van Loosdrecht M, Nielsen PH, Seviour TW, Lin Y. Rethinking characterization, application, and importance of extracellular polymeric substances in water technologies. Curr Opin Biotechnol 2024; 89:103192. [PMID: 39216163 DOI: 10.1016/j.copbio.2024.103192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/20/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024]
Abstract
Biofilms play important roles in water technologies such as membrane treatments and activated sludge. The extracellular polymeric substances (EPS) are key components of biofilms. However, the precise nature of these substances and how they influence biofilm formation and behavior remain critical knowledge gaps. EPS are produced by many different microorganisms and span multiple biopolymer classes, which each require distinct strategies for characterization. The biopolymers additionally associate with each other to form insoluble complexes. Here, we explore recent progress toward resolving the structures and functions of EPS, where a shift towards direct functional assessments and advanced characterization techniques is necessary. This will enable integration with better microbial community and omics analyses to understand EPS biosynthesis pathways and create further opportunities for EPS control and valorization.
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Affiliation(s)
- Sasmitha A Zahra
- Department of Biological and Chemical Engineering, Aarhus University, 8000 Aarhus, Denmark
| | - Rozalia Persiani
- Department of Biotechnology, Delft University of Technology, 2628 Delft, the Netherlands
| | - Morten Kd Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Mark van Loosdrecht
- Department of Biotechnology, Delft University of Technology, 2628 Delft, the Netherlands
| | - Per H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Thomas W Seviour
- Department of Biological and Chemical Engineering, Aarhus University, 8000 Aarhus, Denmark.
| | - Yuemei Lin
- Department of Biotechnology, Delft University of Technology, 2628 Delft, the Netherlands.
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2
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Wang J, Hao S, Ren Q. Uncultured Microorganisms and Their Functions in the Fermentation Systems of Traditional Chinese Fermented Foods. Foods 2023; 12:2691. [PMID: 37509783 PMCID: PMC10378637 DOI: 10.3390/foods12142691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 07/04/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Traditional Chinese fermented foods are diverse and loved by people for their rich nutrition and unique flavors. In the fermentation processes of these foods, the microorganisms in the fermentation systems play a crucial role in determining the flavor and quality. Currently, some microorganisms in the fermentation systems of traditional Chinese fermented foods are in a state of being unculturable or difficult to culture, which hinders the comprehensive analysis and resource development of the microbial communities in the fermentation systems. This article provides an overview of the uncultured microorganisms in the natural environment, in the fermentation systems of traditional Chinese fermented foods, and the research methods for studying such microorganisms. It also discusses the prospects of utilizing the uncultured microorganisms in the fermentation systems of traditional Chinese fermented foods. The aim is to gain a comprehensive understanding of the microbial diversity and uncultured microorganisms in the fermentation systems of traditional Chinese fermented foods in order to better exploit and utilize these microorganisms and promote the development of traditional Chinese fermented foods.
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Affiliation(s)
- Jiaxuan Wang
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing 100048, China
| | - Shuyue Hao
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing 100048, China
| | - Qing Ren
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing 100048, China
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3
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Zheng L, Wang X, Ding A, Yuan D, Tan Q, Xing Y, Xie E. Ecological Insights Into Community Interactions, Assembly Processes and Function in the Denitrifying Phosphorus Removal Activated Sludge Driven by Phosphorus Sources. Front Microbiol 2021; 12:779369. [PMID: 34899660 PMCID: PMC8660105 DOI: 10.3389/fmicb.2021.779369] [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: 09/18/2021] [Accepted: 10/08/2021] [Indexed: 11/29/2022] Open
Abstract
The microbial characteristics in the wastewater treatment plants (WWTPs) strongly affect their optimal performance and functional stability. However, a cognitive gap remains regarding the characteristics of the microbial community driven by phosphorus sources, especially co-occurrence patterns and community assembly based on phylogenetic group. In this study, 59 denitrifying phosphorus removal (DPR) activated sludge samples were cultivated with phosphorus sources. The results suggested that homogeneous selection accounted for the largest proportion that ranged from 35.82 to 64.48%. Deterministic processes dominated in 12 microbial groups (bins): Candidatus_Accumulibacter and Pseudomonas in these bins belonged to phosphate-accumulating organisms (PAOs). Network analysis revealed that species interactions were intensive in cyclic nucleoside phosphate-influenced microbiota. Function prediction indicated that cyclic nucleoside phosphates increased the activity of enzymes related to denitrification and phosphorus metabolism and increased the α-diversity of microorganism but decreased the diversity of metabolic function. Based on these results, it was assumed that cyclic nucleoside phosphates, rather than inorganic phosphates, are the most available phosphorus source for majority microorganisms in DPR activated sludge. The study revealed the important role of phosphorus source in the construction and assembly of microbial communities and provided new insights about pollutant removal from WWTPs.
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Affiliation(s)
- Lei Zheng
- College of Water Sciences, Beijing Normal University, Beijing, China
| | - Xue Wang
- College of Water Sciences, Beijing Normal University, Beijing, China
| | - Aizhong Ding
- College of Water Sciences, Beijing Normal University, Beijing, China
| | - Dongdan Yuan
- College of Water Sciences, Beijing Normal University, Beijing, China
| | - Qiuyang Tan
- College of Water Sciences, Beijing Normal University, Beijing, China
| | - Yuzi Xing
- College of Water Sciences, Beijing Normal University, Beijing, China
| | - En Xie
- College of Water Resources and Civil Engineering, China Agricultural University, Beijing, China
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4
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Cahn JKB, Piel J. Anwendungen von Einzelzellmethoden in der mikrobiellen Naturstoffforschung. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.201900532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jackson K. B. Cahn
- Institut für Mikrobiologie Eidgenössische Technische Hochschule Zürich (ETH) 8093 Zürich Schweiz
| | - Jörn Piel
- Institut für Mikrobiologie Eidgenössische Technische Hochschule Zürich (ETH) 8093 Zürich Schweiz
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5
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Cahn JKB, Piel J. Opening up the Single-Cell Toolbox for Microbial Natural Products Research. Angew Chem Int Ed Engl 2021; 60:18412-18428. [PMID: 30748086 DOI: 10.1002/anie.201900532] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Indexed: 02/06/2023]
Abstract
The diverse microbes that produce natural products represent an important source of novel therapeutics, drug leads, and scientific tools. However, the vast majority have not been grown in axenic culture and are members of complex communities. While meta-'omic methods such as metagenomics, -transcriptomics, and -proteomics reveal collective molecular features of this "microbial dark matter", the study of individual microbiome members can be challenging. To address these limits, a number of techniques with single-bacterial resolution have been developed in the last decade and a half. While several of these are embraced by microbial ecologists, there has been less use by researchers interested in mining microbes for natural products. In this review, we discuss the available and emerging techniques for targeted single-cell analysis with a particular focus on applications to the discovery and study of natural products.
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Affiliation(s)
- Jackson K B Cahn
- Instit. of Microbiol., Eidgenössische Technische Hochschule Zürich (ETH), 8093, Zurich, Switzerland
| | - Jörn Piel
- Instit. of Microbiol., Eidgenössische Technische Hochschule Zürich (ETH), 8093, Zurich, Switzerland
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6
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Li D, Liang X, Li Z, Jin Y, Zhou R, Wu C. Effect of chemical oxygen demand load on the nitrification and microbial communities in activated sludge from an aerobic nitrifying reactor. Can J Microbiol 2019; 66:59-70. [PMID: 31644885 DOI: 10.1139/cjm-2018-0599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, we explored the effect of chemical oxygen demand (COD) load on the nitrification and microbial communities in activated sludge isolated from an aerobic nitrifying tank. The activated sludge was cultured in three different COD groups: L-COD, 200 mg/L; M-COD, 1200 mg/L; H-COD, 4200 mg/L. The results indicated that the COD exerts a negligible effect on the nitrogen removal ability within the first 24 h. However, the nitrification rate decreased with culture time; the ammonium degradation rates were found to be 80.26%, 57.56%, and 43.43% at 72 h in the three COD groups, respectively. These values correspond to decreases of 19.40%, 41.83%, and 51.48%, respectively, in relation to those observed at 24 h. The activated sludge in the different COD groups exhibited similar community compositions after 24 h, as assessed by Illumina high-throughput sequencing, while a significant difference in the relative abundances of some organisms occurred after 48 and 72 h. Proteobacteria was the main phylum, with a relative abundance of >51.45%. The genera Aridibacter, Paracoccus, Nitrospira, and Nitrosomonas were suppressed by COD load over time. This study may contribute to our knowledge about the nitrification ability and microbial communities in activated sludge at different COD load levels.
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Affiliation(s)
- Dan Li
- College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China.,College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China
| | - Xihong Liang
- College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China.,College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China
| | - Zhengwei Li
- College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China.,College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China
| | - Yao Jin
- College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China.,College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China
| | - Rongqing Zhou
- College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China.,College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China
| | - Chongde Wu
- College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China.,College of Light Industry, Textile & Food Engineering, Sichuan University, Chengdu 610065, P.R. China; Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu 610065, P.R. China
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7
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Folch-Mallol JL, Zárate A, Sánchez-Reyes A, López-Lara IM. Expression, purification, and characterization of a metagenomic thioesterase from activated sludge involved in the degradation of acylCoA-derivatives. Protein Expr Purif 2019; 159:49-52. [PMID: 30905871 DOI: 10.1016/j.pep.2019.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/14/2019] [Accepted: 03/18/2019] [Indexed: 12/28/2022]
Abstract
Metagenomic libraries are a novel and powerful approach to seek for pathways involved in xenobiotic degradation, since this technique abolishes the need for cultivating microorganisms that otherwise would be overlooked if they cannot grow on standard laboratory media and conditions. In this paper, we describe the expression, purification and characterization of a novel metagenomic thioesterase which was described to be involved in phenylacetic acid degradation (A. Sánchez-Reyes, R. Batista-García, G. Valdés-García E. Ortiz, L. Perezgasga, A. Zárate-Romero, N. Pastor, J. L. Folch-Mallol, A Family 13 thioesterase isolated from an activated sludge metagenome: insights into aromatic compounds metabolism, Proteins 85 (2017) 1222-1237). According to similarity and phylogenetic analyses, the enzyme seems to belong to an Actinobacterium. Nevertheless, after a process of denaturation and refolding, the protein expressed in E. coli was obtained in an active form. New data concerning the substrate preferences for this enzyme are presented which suggest that this thioesterase could be involved in breaking the ester bond in the CoA-linear acyl derivatives of the phenylacetic acetic pathway.
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Affiliation(s)
- Jorge Luis Folch-Mallol
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av Universidad 1001, Colonia Chamilpa, Cuernavaca, 62209, Morelos, Mexico.
| | - Andrés Zárate
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av Universidad 1001, Colonia Chamilpa, Cuernavaca, 62209, Morelos, Mexico
| | - Ayixón Sánchez-Reyes
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av Universidad 1001, Colonia Chamilpa, Cuernavaca, 62209, Morelos, Mexico
| | - Isabel M López-Lara
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av Universidad 1001, Colonia Chamilpa, Cuernavaca, 62209, Morelos, Mexico
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8
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Safford HR, Bischel HN. Flow cytometry applications in water treatment, distribution, and reuse: A review. WATER RESEARCH 2019; 151:110-133. [PMID: 30594081 DOI: 10.1016/j.watres.2018.12.016] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/30/2018] [Accepted: 12/01/2018] [Indexed: 06/09/2023]
Abstract
Ensuring safe and effective water treatment, distribution, and reuse requires robust methods for characterizing and monitoring waterborne microbes. Methods widely used today can be limited by low sensitivity, high labor and time requirements, susceptibility to interference from inhibitory compounds, and difficulties in distinguishing between viable and non-viable cells. Flow cytometry (FCM) has recently gained attention as an alternative approach that can overcome many of these challenges. This article critically and systematically reviews for the first time recent literature on applications of FCM in water treatment, distribution, and reuse. In the review, we identify and examine nearly 300 studies published from 2000 to 2018 that illustrate the benefits and challenges of using FCM for assessing source-water quality and impacts of treatment-plant discharge on receiving waters, wastewater treatment, drinking water treatment, and drinking water distribution. We then discuss options for combining FCM with other indicators of water quality and address several topics that cut across nearly all applications reviewed. Finally, we identify priority areas in which more work is needed to realize the full potential of this approach. These include optimizing protocols for FCM-based analysis of waterborne viruses, optimizing protocols for specifically detecting target pathogens, automating sample handling and preparation to enable real-time FCM, developing computational tools to assist data analysis, and improving standards for instrumentation, methods, and reporting requirements. We conclude that while more work is needed to realize the full potential of FCM in water treatment, distribution, and reuse, substantial progress has been made over the past two decades. There is now a sufficiently large body of research documenting successful applications of FCM that the approach could reasonably and realistically see widespread adoption as a routine method for water quality assessment.
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Affiliation(s)
- Hannah R Safford
- Department of Civil and Environmental Engineering, University of California Davis, 2001 Ghausi Hall, 480 Bainer Hall Drive, 95616, Davis, CA, United States
| | - Heather N Bischel
- Department of Civil and Environmental Engineering, University of California Davis, 2001 Ghausi Hall, 480 Bainer Hall Drive, 95616, Davis, CA, United States.
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9
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Huys GR, Raes J. Go with the flow or solitary confinement: a look inside the single-cell toolbox for isolation of rare and uncultured microbes. Curr Opin Microbiol 2018; 44:1-8. [PMID: 29908491 DOI: 10.1016/j.mib.2018.05.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/24/2018] [Indexed: 01/01/2023]
Abstract
With the vast majority of the microbial world still considered unculturable or undiscovered, microbiologists not only require more fundamental insights concerning microbial growth requirements but also need to implement miniaturized, versatile and high-throughput technologies to upscale current microbial isolation strategies. In this respect, single-cell-based approaches are increasingly finding their way to the microbiology lab. A number of recent studies have demonstrated that analysis and separation of free microbial cells by flow-based sorting as well as physical stochastic confinement of individual cells in microenvironment compartments can facilitate the isolation of previously uncultured species and the discovery of novel microbial taxa. Still, while most of these methods give immediate access to downstream whole genome sequencing, upscaling to higher cell densities as required for metabolic readouts and preservation purposes can remain challenging. Provided that these and other technological challenges are addressed in future innovation rounds, integration of single-cell tools in commercially available benchtop instruments and service platforms is expected to trigger more targeted explorations in the microbial dark matter at a depth comparable to metagenomics.
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Affiliation(s)
- Geert Rb Huys
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium; VIB, Center for Microbiology, Leuven, Belgium
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium; VIB, Center for Microbiology, Leuven, Belgium.
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10
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Xia J, Ye L, Ren H, Zhang XX. Microbial community structure and function in aerobic granular sludge. Appl Microbiol Biotechnol 2018; 102:3967-3979. [PMID: 29550989 DOI: 10.1007/s00253-018-8905-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/22/2018] [Accepted: 02/26/2018] [Indexed: 12/28/2022]
Abstract
Aerobic granular sludge (AGS), a self-immobilized microbial consortium containing different functional microorganisms, is receiving growing attention, since it has shown great technological and economical potentials in the field of wastewater treatment. Microbial community is crucial for the formation, stability, and pollutant removal efficiency of aerobic granules. This mini-review systematically summarizes the recent findings of the microbial community structure and function of AGS and discusses the new research progress in the microbial community dynamics during the granulation process and spatial distribution patterns of the microbiota in AGS. The presented information may be helpful for the in-depth theoretical study and practical application of AGS technology in the future.
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Affiliation(s)
- Juntao Xia
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China.
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China.
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11
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Zhou Y, Lisowski W, Zhou Y, Jern NW, Huang K, Fong E. Genetic improvement of Magnetospirillum gryphiswaldense for enhanced biological removal of phosphate. Biotechnol Lett 2017; 39:1509-1514. [PMID: 28660385 DOI: 10.1007/s10529-017-2383-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/21/2017] [Indexed: 11/25/2022]
Abstract
OBJECTIVES To improve its phosphate accumulating abilities for phosphate recycling from wastewater, a magnetotactic bacterium, Magnetospirillum gryphiswaldense, was genetically modified to over-express polyphosphate kinase. RESULTS Polyphosphate kinase was over-expressed in the bacterium. The recombinant strain accumulated ninefold more polyphosphate from synthetic wastewater compared to original wild type. The magnetic property of the recombinant M. gryphiswaldense strain was retained. CONCLUSIONS The recombinant M. gryphiswaldense can be used for phosphate removal and recovery in bioremediation.
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Affiliation(s)
- Yanping Zhou
- College of Electronics and Information Engineering, Sichuan University, Chengdu, 610065, China
| | - Wiktor Lisowski
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Yan Zhou
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 CleanTech Loop, Singapore, 637141, Singapore
| | - Ng Wun Jern
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 CleanTech Loop, Singapore, 637141, Singapore
| | - Kama Huang
- College of Electronics and Information Engineering, Sichuan University, Chengdu, 610065, China
| | - Eileen Fong
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore.
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12
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An on-chip imaging droplet-sorting system: a real-time shape recognition method to screen target cells in droplets with single cell resolution. Sci Rep 2017; 7:40072. [PMID: 28059147 PMCID: PMC5216404 DOI: 10.1038/srep40072] [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: 09/16/2016] [Accepted: 11/30/2016] [Indexed: 12/29/2022] Open
Abstract
A microfluidic on-chip imaging cell sorter has several advantages over conventional cell sorting methods, especially to identify cells with complex morphologies such as clusters. One of the remaining problems is how to efficiently discriminate targets at the species level without labelling. Hence, we developed a label-free microfluidic droplet-sorting system based on image recognition of cells in droplets. To test the applicability of this method, a mixture of two plankton species with different morphologies (Dunaliella tertiolecta and Phaeodactylum tricornutum) were successfully identified and discriminated at a rate of 10 Hz. We also examined the ability to detect the number of objects encapsulated in a droplet. Single cell droplets sorted into collection channels showed 91 ± 4.5% and 90 ± 3.8% accuracy for D. tertiolecta and P. tricornutum, respectively. Because we used image recognition to confirm single cell droplets, we achieved highly accurate single cell sorting. The results indicate that the integrated method of droplet imaging cell sorting can provide a complementary sorting approach capable of isolating single target cells from a mixture of cells with high accuracy without any staining.
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13
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Abe T, Ushiki N, Fujitani H, Tsuneda S. A rapid collection of yet unknown ammonia oxidizers in pure culture from activated sludge. WATER RESEARCH 2017; 108:169-178. [PMID: 27836171 DOI: 10.1016/j.watres.2016.10.070] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 06/06/2023]
Abstract
Nitrification is an important reaction in the biological nitrogen removal process in wastewater treatment plants (WWTPs). As ammonia-oxidizing microbes are slow-growing and sensitive to environmental factors such as free ammonia, pure strains are hard to obtain, preventing our understanding of their physiological characteristics. To conquer this hurdle, we report a high-throughput isolation technique based on scattering signatures, which exploits the tendency of many ammonia-oxidizing bacteria (AOB) to form microcolonies in activated sludge. The AOB microcolonies were directly sorted from the activated sludge without long incubation and enrichment bias, and were sequentially inoculated into 96-well microtiter plates containing growth medium. Phylogenetic analysis of the pure strains isolated in this study revealed a deeply branching and unrecognized lineage and diversity within the genus Nitrosomonas, beyond our expectation.
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Affiliation(s)
- Takuma Abe
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Norisuke Ushiki
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hirotsugu Fujitani
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
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14
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Riba J, Gleichmann T, Zimmermann S, Zengerle R, Koltay P. Label-free isolation and deposition of single bacterial cells from heterogeneous samples for clonal culturing. Sci Rep 2016; 6:32837. [PMID: 27596612 PMCID: PMC5011771 DOI: 10.1038/srep32837] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 08/16/2016] [Indexed: 01/11/2023] Open
Abstract
The isolation and analysis of single prokaryotic cells down to 1 μm and less in size poses a special challenge and requires micro-engineered devices to handle volumes in the picoliter to nanoliter range. Here, an advanced Single-Cell Printer (SCP) was applied for automated and label-free isolation and deposition of bacterial cells encapsulated in 35 pl droplets by inkjet-like printing. To achieve this, dispenser chips to generate micro droplets have been fabricated with nozzles 20 μm in size. Further, the magnification of the optical system used for cell detection was increased. Redesign of the optical path allows for collision-free addressing of any flat substrate since no compartment protrudes below the nozzle of the dispenser chip anymore. The improved system allows for deterministic isolation of individual bacterial cells. A single-cell printing efficiency of 93% was obtained as shown by printing fluorescent labeled E. coli. A 96-well plate filled with growth medium is inoculated with single bacteria cells on average within about 8 min. Finally, individual bacterial cells from a heterogeneous sample of E. coli and E. faecalis were isolated for clonal culturing directly on agar plates in user-defined array geometry.
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Affiliation(s)
- J Riba
- Laboratory for MEMS Applications, Department of Microsystems Engineering-IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - T Gleichmann
- Laboratory for MEMS Applications, Department of Microsystems Engineering-IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - S Zimmermann
- Laboratory for MEMS Applications, Department of Microsystems Engineering-IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - R Zengerle
- Laboratory for MEMS Applications, Department of Microsystems Engineering-IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.,Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.,BIOSS - Centre for Biological Signalling Studies, University of Freiburg, 79110 Freiburg, Germany
| | - P Koltay
- Laboratory for MEMS Applications, Department of Microsystems Engineering-IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
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