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Zhao Y, Park I, Rubakhin SS, Bashir R, Vlasov Y, Sweedler JV. 1-Octanol-assisted ultra-small volume droplet microfluidics with nanoelectrospray ionization mass spectrometry. Anal Chim Acta 2024; 1321:342998. [PMID: 39155094 DOI: 10.1016/j.aca.2024.342998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 07/18/2024] [Accepted: 07/20/2024] [Indexed: 08/20/2024]
Abstract
BACKGROUND Droplet microfluidics with push-pull and microdialysis sampling from brain slices, cultured cells and engineered tissues produce low volume mass limited samples containing analytes sampled from the extracellular space. This sampling approach coupled to mass spectrometry (MS) detection allows evaluation of time-dependent chemical changes. Our goal is an approach for continuous sampling and segregation of extracellular samples into picoliter droplets followed by the characterization of the droplets using nanoelectrospray ionization (nESI) MS. The main focus here is the optimization of the carrier oil for the microfluidic device that neither affects the stability of picoliter droplets nor compatibility with MS detection of a range of analytes. RESULTS We developed and characterized a 1-octanol-assisted ultra-small volume droplet microfluidic nESI MS system for the analysis of neurotransmitters in distinct samples including cerebrospinal fluid (CSF). The use of a 1-octanol oil phase was effective for generation of aqueous droplets as small as 65 pL and enabled detection of acetylcholine (ACh) and gamma-aminobutyric acid (GABA) in water and artificial CSF. Continuous MS analysis of droplets for extended periods up to 220 min validated the long-term stability of droplet generation and analyte detection by nESI-MS. As an example, ACh response demonstrated a linear working range (R2 = 0.99) between 0.4 μM and 25 μM with a limit of detection of 370 nM (24 amol), enabling its quantitation in rodent CSF. SIGNIFICANCE The established droplet microfluidics - nESI MS approach allows the analysis of microenvironments at high spatiotemporal resolution. The approach may allow microsampling and monitoring of spatiotemporal dynamics of neurochemicals and drugs in the brain and spinal cord of live animals.
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Affiliation(s)
- Yaoyao Zhao
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Insu Park
- Holonyak Micro & Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Stanislav S Rubakhin
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Rashid Bashir
- Beckman Institute for Advanced Science and Technology, Holonyak Micro & Nanotechnology Laboratory, and Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yurii Vlasov
- Beckman Institute for Advanced Science and Technology, Holonyak Micro & Nanotechnology Laboratory, and Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jonathan V Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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2
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Guo X, Ren J, Zhou X, Zhang M, Lei C, Chai R, Zhang L, Lu D. Strategies to improve the efficiency and quality of mutant breeding using heavy-ion beam irradiation. Crit Rev Biotechnol 2024; 44:735-752. [PMID: 37455421 DOI: 10.1080/07388551.2023.2226339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 04/15/2023] [Indexed: 07/18/2023]
Abstract
Heavy-ion beam irradiation (HIBI) is useful for generating new germplasm in plants and microorganisms due to its ability to induce high mutagenesis rate, broad mutagenesis spectrum, and excellent stability of mutants. However, due to the random mutagenesis and associated mutant breeding modalities, it is imperative to improve HIBI-based mutant breeding efficiency and quality. This review discusses and summarizes the findings of existing theoretical and technical studies and presents a set of tandem strategies to enable efficient and high-quality HIBI-based mutant breeding practices. These strategies: adjust the mutation-inducing techniques, regulate cellular response states, formulate high-throughput screening schemes, and apply the generated superior genetic elements to genetic engineering approaches, thereby, improving the implications and expanding the scope of HIBI-based mutant breeding. These strategies aim to improve the mutagenesis rate, screening efficiency, and utilization of positive mutations. Here, we propose a model based on the integration of these strategies that would leverage the advantages of HIBI while compensating for its present shortcomings. Owing to the unique advantages of HIBI in creating high-quality genetic resources, we believe this review will contribute toward improving HIBI-based breeding.
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Affiliation(s)
- Xiaopeng Guo
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Junle Ren
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiang Zhou
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Miaomiao Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cairong Lei
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ran Chai
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Lingxi Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Dong Lu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
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3
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Wu R, Ji P, Hua Y, Li H, Zhang W, Wei Y. Research progress in isolation and identification of rumen probiotics. Front Cell Infect Microbiol 2024; 14:1411482. [PMID: 38836057 PMCID: PMC11148321 DOI: 10.3389/fcimb.2024.1411482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 04/30/2024] [Indexed: 06/06/2024] Open
Abstract
With the increasing research on the exploitation of rumen microbial resources, rumen probiotics have attracted much attention for their positive contributions in promoting nutrient digestion, inhibiting pathogenic bacteria, and improving production performance. In the past two decades, macrogenomics has provided a rich source of new-generation probiotic candidates, but most of these "dark substances" have not been successfully cultured due to the restrictive growth conditions. However, fueled by high-throughput culture and sorting technologies, it is expected that the potential probiotics in the rumen can be exploited on a large scale, and their potential applications in medicine and agriculture can be explored. In this paper, we review and summarize the classical techniques for isolation and identification of rumen probiotics, introduce the development of droplet-based high-throughput cell culture and single-cell sequencing for microbial culture and identification, and finally introduce promising cultureomics techniques. The aim is to provide technical references for the development of related technologies and microbiological research to promote the further development of the field of rumen microbiology research.
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Affiliation(s)
| | - Peng Ji
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | | | | | | | - Yanming Wei
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
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4
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Wu X, Xie B, Qiao Y, Yuan S, Du W. μMET: A Novel Reusable Microfluidic Chip for Precision Microbial Enumeration Tests. Anal Chem 2024; 96:630-635. [PMID: 38163292 DOI: 10.1021/acs.analchem.3c04889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
This work describes μMET, a novel microfluidic device for precise microbial enumeration tests (MET), essential in pharmaceutical, cosmetic, and food industries for ensuring microbiological safety standards. The μMET chip, comprising two hydrophobic glass plates, features a 15-μm deep μMET chamber enhanced by nanopillars and air supply units, facilitating both immediate and growth-dependent MET. Experimental results, with E. coli as a model bacterium, demonstrate that μMET provides counting linearity that outperforms traditional hemocytometers. The chip's design mitigates challenges like evaporation and ensures high-resolution imaging, making it a cost-effective and reusable alternative to conventional methods. Notably, bright-field μMET eliminates the need for fluorescent staining, streamlining operations with deep-learning algorithms for bacterial counts. Furthermore, we have developed a high-parallel μMET chip featuring 16 counting chambers, enhancing throughput and accommodating immediate and growth-dependent MET approaches. Its innovative design and adaptability render the μMET chip as a valuable tool for microbiology, medicine, and industry applications.
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Affiliation(s)
- Xiaolin Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences and Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 10049, China
| | - Bingliang Xie
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences and Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 10049, China
| | - Yuxin Qiao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuai Yuan
- China National Pharmaceutical Foreign Trade Corporation, Beijing 100029, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences and Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 10049, China
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5
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Wang M, Zheng N, Li X, Zhao K, Xie BB. Enrichment Pretreatment Expands the Microbial Diversity Cultivated from Marine Sediments. Microorganisms 2023; 11:2771. [PMID: 38004782 PMCID: PMC10673404 DOI: 10.3390/microorganisms11112771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
The majority of the microbial diversity in nature has not been recovered through cultivation. Enrichment is a classical technique widely used in the selective cultivation of specific taxa. Whether enrichment is suitable for cultivation studies that aim to recover large numbers of species remains little explored. To address this issue, we evaluated the potential of enrichment pretreatment in the cultivation of bacteria from marine sediments. Upon obtaining and classifying a total of 943 pure cultures from chitin and cellulose enrichment pretreatment systems and a control system, our results showed that species obtained using enrichment pretreatment differed greatly from those without enrichment. Multiple enrichment media and different enrichment times increased the number of cultivated species in a sample. Amplicon sequencing showed that the increased relative abundance during pretreatment contributed greatly to bacterial cultivation. The testing of degradation abilities against chitin and cellulose and the whole-genome sequencing of representative strains suggested that microorganism-microorganism interactions play roles in the expanded diversity of cultivated bacteria. This study provides new insights into the abilities of enrichment in exploring cultivable diversity and mining microbial resources.
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Affiliation(s)
| | | | | | | | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (M.W.); (N.Z.); (X.L.); (K.Z.)
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6
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Muta M, Kawakubo W, Yoon DH, Tanaka D, Sekiguchi T, Shoji S, Ito M, Hatada Y, Funatsu T, Iizuka R. Deformability-Based Microfluidic Microdroplet Screening to Obtain Agarolytic Bacterial Cells. Anal Chem 2023; 95:16107-16114. [PMID: 37877901 DOI: 10.1021/acs.analchem.3c02174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Environmental microorganisms possess enzymes that can digest macromolecules such as agarose into smaller molecules that can be utilized for growth. These enzymes could be valuable for the effective utilization of global resources. However, since most of the microorganisms on Earth remain uncultured, there is significant untapped enzymatic potential in nature. Therefore, it is necessary to develop innovative tools and strategies for exploring these enzymatic resources. To address this, we developed a method for screening microbial cells that secrete hydrogel-degrading enzymes using deformability-based microfluidic microdroplet sorting. In this method, microbial cells are encapsulated as single cells in water-in-oil (W/O) microdroplets with a hydrogel whose shape becomes deformable as the hydrogel is progressively degraded into smaller molecules. Screening is achieved using a microfluidic device that passively sorts the deformed W/O microdroplets. Using this method, we successfully sorted agarose-containing microdroplets, encapsulating single bacterial cells that hydrolyzed agarose. This method can be used to screen various hydrogel-degrading microbial cells.
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Affiliation(s)
- Mikihisa Muta
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Wataru Kawakubo
- Faculty of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Dong Hyun Yoon
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda Tsurumakicho, Shinjuku-ku, Tokyo 162-0041, Japan
| | - Daiki Tanaka
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda Tsurumakicho, Shinjuku-ku, Tokyo 162-0041, Japan
| | - Tetsushi Sekiguchi
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda Tsurumakicho, Shinjuku-ku, Tokyo 162-0041, Japan
| | - Shuichi Shoji
- Faculty of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda Tsurumakicho, Shinjuku-ku, Tokyo 162-0041, Japan
| | - Mei Ito
- Department of Life Science and Green Chemistry, Faculty of Engineering, Saitama Institute of Technology, 1690 Fusaiji, Fukaya-shi 369-0293, Saitama, Japan
| | - Yuji Hatada
- Department of Life Science and Green Chemistry, Faculty of Engineering, Saitama Institute of Technology, 1690 Fusaiji, Fukaya-shi 369-0293, Saitama, Japan
| | - Takashi Funatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ryo Iizuka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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7
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Qian J, Lan H, Huang L, Zheng S, Hu X, Chen M, Lee JEY, Zhang W. Acoustofluidics for simultaneous droplet transport and centrifugation facilitating ultrasensitive biomarker detection. LAB ON A CHIP 2023; 23:4343-4351. [PMID: 37718921 DOI: 10.1039/d3lc00626c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Trace biological sample detection is critical for the analysis of pathologies in biomedicine. Integration of microfluidic manipulation techniques typically strengthens biosensing performance. For instance, using isothermal amplification reactions to sense trace miRNA in peripheral circulation lacks a sufficiently complex pretreatment process that limits the sensitivity of on-chip detection. Herein we propose an orthogonal tunable acoustic tweezer (OTAT) to simultaneously actuate the transportation and centrifugation of μ-droplets on a single device. The OTAT enables diversified modes of droplet transportation such as unidirectional transport, multi-direction transport, round-trip transport, tilt angle movement, multi-droplet fusion, and continuous centrifugation of the dynamic droplets simultaneously. The multiplicity of modalities enables the focusing of a loaded analyte at the center of the droplet or constant rotation about the center axis of the droplet. We herein demonstrate the OTAT's ability to actuate transportation, fusion, and centrifugation-based pretreatment of two biological sample droplets loaded with miRNA biomarkers and multiple mixtures, as well as facilitating the increase of fluorescence detection sensitivity by an order of magnitude compared to traditional tube reaction methods. The results herein demonstrate the OTAT-based droplet acoustofluidic platform's ability to combine a wide range of biosensing mechanisms and provide a higher accuracy of detection for one-stop point-of-care disease diagnosis.
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Affiliation(s)
- Jingui Qian
- Anhui Province Key Laboratory of Measuring Theory and Precision Instrument, School of Instrument Science and Opto-Electronics Engineering, Hefei University of Technology, Hefei 230009, China.
| | - Huaize Lan
- Anhui Province Key Laboratory of Measuring Theory and Precision Instrument, School of Instrument Science and Opto-Electronics Engineering, Hefei University of Technology, Hefei 230009, China.
| | - Liang Huang
- Anhui Province Key Laboratory of Measuring Theory and Precision Instrument, School of Instrument Science and Opto-Electronics Engineering, Hefei University of Technology, Hefei 230009, China.
| | - Shaohui Zheng
- School of Medical Imaging, Xuzhou Medical University, Xuzhou 221006, China.
| | - Xuefeng Hu
- Anhui Province Key Laboratory of Measuring Theory and Precision Instrument, School of Instrument Science and Opto-Electronics Engineering, Hefei University of Technology, Hefei 230009, China.
| | - Minghui Chen
- School of Medical Imaging, Xuzhou Medical University, Xuzhou 221006, China.
| | - Joshua E-Y Lee
- School of Electrical and Data Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Wei Zhang
- School of Physics and Optoelectronic Engineering, Guangdong University of Technology, Guangzhou 510006, China.
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Vitalis C, Wenzel T. Leveraging interactions in microfluidic droplets for enhanced biotechnology screens. Curr Opin Biotechnol 2023; 82:102966. [PMID: 37390513 DOI: 10.1016/j.copbio.2023.102966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 07/02/2023]
Abstract
Microfluidic droplet screens serve as an innovative platform for high-throughput biotechnology, enabling significant advancements in discovery, product optimization, and analysis. This review sheds light on the emerging trends of interaction assays in microfluidic droplets, underscoring the unique suitability of droplets for these applications. Encompassing a diverse range of biological entities such as antibodies, enzymes, DNA, RNA, various microbial and mammalian cell types, drugs, and other molecules, these assays demonstrate their versatility and scope. Recent methodological breakthroughs have escalated these screens to novel scales of bioanalysis and biotechnological product design. Moreover, we highlight pioneering advancements that extend droplet-based screens into new domains: cargo delivery within human bodies, application of synthetic gene circuits in natural environments, 3D printing, and the development of droplet structures responsive to environmental signals. The potential of this field is profound and only set to increase.
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Affiliation(s)
- Carolus Vitalis
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul 7820244, Santiago, Chile
| | - Tobias Wenzel
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul 7820244, Santiago, Chile.
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9
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De Figueiredo I, Bartenlian B, Van der Rest G, Pallandre A, Halgand F. Proteomics Methodologies: The Search of Protein Biomarkers Using Microfluidic Systems Coupled to Mass Spectrometry. Proteomes 2023; 11:proteomes11020019. [PMID: 37218924 DOI: 10.3390/proteomes11020019] [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: 03/23/2023] [Revised: 04/29/2023] [Accepted: 05/07/2023] [Indexed: 05/24/2023] Open
Abstract
Protein biomarkers have been the subject of intensive studies as a target for disease diagnostics and monitoring. Indeed, biomarkers have been extensively used for personalized medicine. In biological samples, these biomarkers are most often present in low concentrations masked by a biologically complex proteome (e.g., blood) making their detection difficult. This complexity is further increased by the needs to detect proteoforms and proteome complexity such as the dynamic range of compound concentrations. The development of techniques that simultaneously pre-concentrate and identify low-abundance biomarkers in these proteomes constitutes an avant-garde approach to the early detection of pathologies. Chromatographic-based methods are widely used for protein separation, but these methods are not adapted for biomarker discovery, as they require complex sample handling due to the low biomarker concentration. Therefore, microfluidics devices have emerged as a technology to overcome these shortcomings. In terms of detection, mass spectrometry (MS) is the standard analytical tool given its high sensitivity and specificity. However, for MS, the biomarker must be introduced as pure as possible in order to avoid chemical noise and improve sensitivity. As a result, microfluidics coupled with MS has become increasingly popular in the field of biomarker discovery. This review will show the different approaches to protein enrichment using miniaturized devices and the importance of their coupling with MS.
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Affiliation(s)
- Isabel De Figueiredo
- Institut de Chimie Physique, Université Paris Saclay, Avenue Jean Perrin, F91400 Orsay, France
| | - Bernard Bartenlian
- Centre des Nanosciences et Nanotechnologies, Université Paris Saclay, 10 Boulevard Thomas Gobert, F91120 Palaiseau, France
| | - Guillaume Van der Rest
- Institut de Chimie Physique, Université Paris Saclay, Avenue Jean Perrin, F91400 Orsay, France
| | - Antoine Pallandre
- Institut de Chimie Physique, Université Paris Saclay, Avenue Jean Perrin, F91400 Orsay, France
| | - Frédéric Halgand
- Institut de Chimie Physique, Université Paris Saclay, Avenue Jean Perrin, F91400 Orsay, France
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Baranova AA, Alferova VA, Korshun VA, Tyurin AP. Modern Trends in Natural Antibiotic Discovery. Life (Basel) 2023; 13:life13051073. [PMID: 37240718 DOI: 10.3390/life13051073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/10/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Natural scaffolds remain an important basis for drug development. Therefore, approaches to natural bioactive compound discovery attract significant attention. In this account, we summarize modern and emerging trends in the screening and identification of natural antibiotics. The methods are divided into three large groups: approaches based on microbiology, chemistry, and molecular biology. The scientific potential of the methods is illustrated with the most prominent and recent results.
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Affiliation(s)
- Anna A Baranova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, 119021 Moscow, Russia
| | - Vera A Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, 119021 Moscow, Russia
| | - Vladimir A Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Anton P Tyurin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
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11
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Jian X, Guo X, Cai Z, Wei L, Wang L, Xing XH, Zhang C. Single-cell microliter-droplet screening system (MISS Cell): An integrated platform for automated high-throughput microbial monoclonal cultivation and picking. Biotechnol Bioeng 2023; 120:778-792. [PMID: 36477904 DOI: 10.1002/bit.28300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/18/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022]
Abstract
Solid plates have been used for microbial monoclonal isolation, cultivation, and colony picking since 1881. However, the process is labor- and resource-intensive for high-throughput requirements. Currently, several instruments have been integrated for automated and high-throughput picking, but complicated and expensive. To address these issues, we report a novel integrated platform, the single-cell microliter-droplet screening system (MISS Cell), for automated, high-throughput microbial monoclonal colony cultivation and picking. We verified the monoclonality of droplet cultures in the MISS Cell and characterized culture performance. Compared with solid plates, the MISS Cell generated a larger number of monoclonal colonies with higher initial growth rates using fewer resources. Finally, we established a workflow for automated high-throughput screening of Corynebacterium glutamicum using the MISS Cell and identified high glutamate-producing strains. The MISS Cell can serve as a universal platform to efficiently produce monoclonal colonies in high-throughput applications, overcoming the limitations of solid plates to promote rapid development in biotechnology.
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Affiliation(s)
- Xingjin Jian
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China.,Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China
| | - Xiaojie Guo
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China.,Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China
| | - Zhengshuo Cai
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China.,Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China
| | - Longfeng Wei
- College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
| | - Liyan Wang
- Luoyang TMAXTREE Biotechnology Co., Ltd., Luoyang, China
| | - Xin-Hui Xing
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China.,Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China
| | - Chong Zhang
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, China.,Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China.,Center for Synthetic & Systems Biology, Tsinghua University, Beijing, China
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12
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Wang B, Liu W, Liang B, Jiang J, Wang A. Microbial fingerprints of methanation in a hybrid electric-biological anaerobic digestion. WATER RESEARCH 2022; 226:119270. [PMID: 36323204 DOI: 10.1016/j.watres.2022.119270] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/26/2022] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Abstract
Biomethane as a sustainable, alternative, and carbon-neutral renewable energy source to fossil fuels is highly needed to alleviate the global energy crisis and climate change. The conventional anaerobic digestion (AD) process for biomethane production from waste(water) streams has been widely employed while struggling with a low production rate, low biogas qualities, and frequent instability. The electric-biologically hybrid microbial electrochemical anaerobic digestion system (MEC-AD) prospects more stable and robust biomethane generation, which facilitates complex organic substrates degradation and mediates functional microbial populations by giving a small input power (commonly voltages < 1.0 V), mainly enhancing the communication between electroactive microorganisms and (electro)methanogens. Despite numerous bioreactor tests and studies that have been conducted, based on the MEC-AD systems, the integrated microbial fingerprints, and cooperation, accelerating substrate degradation, and biomethane production, have not been fully summarized. Herein, we present a comprehensive review of this novel developing biotechnology, beginning with the principles of MEC-AD. First, we examine the fundamentals, configurations, classifications, and influential factors of the whole system's performances (reactor types, applied voltages, temperatures, conductive materials, etc.,). Second, extracellular electron transfer either between diverse microbes or between microbes and electrodes for enhanced biomethane production are analyzed. Third, we further conclude (electro)methanogenesis, and microbial interactions, and construct ecological networks of microbial consortia in MEC-AD. Finally, future development and perspectives on MEC-AD for biomethane production are proposed.
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Affiliation(s)
- Bo Wang
- State Key Lab of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, 518055 Shenzhen, China; Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark; Department of Environmental and Resource Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Wenzong Liu
- State Key Lab of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, 518055 Shenzhen, China.
| | - Bin Liang
- State Key Lab of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, 518055 Shenzhen, China
| | - Jiandong Jiang
- Key Lab of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Aijie Wang
- State Key Lab of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, 518055 Shenzhen, China; CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085 Beijing, China
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13
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Leonaviciene G, Mazutis L. RNA cytometry of single-cells using semi-permeable microcapsules. Nucleic Acids Res 2022; 51:e2. [PMID: 36268865 PMCID: PMC9841424 DOI: 10.1093/nar/gkac918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/23/2022] [Accepted: 10/07/2022] [Indexed: 01/29/2023] Open
Abstract
Analytical tools for gene expression profiling of individual cells are critical for studying complex biological systems. However, the techniques enabling rapid measurements of gene expression on thousands of single-cells are lacking. Here, we report a high-throughput RNA cytometry for digital profiling of single-cells isolated in liquid droplets enveloped by a thin semi-permeable membrane (microcapsules). Due to the selective permeability of the membrane, the desirable enzymes and reagents can be loaded, or replaced, in the microcapsule at any given step by simply changing the reaction buffer in which the microcapsules are dispersed. Therefore, complex molecular biology workflows can be readily adapted to conduct nucleic acid analysis on encapsulated mammalian cells, or other biological species. The microcapsules support sequential multi-step enzymatic reactions and remain intact under different biochemical conditions, freezing, thawing, and thermocycling. Combining microcapsules with conventional FACS provides a high-throughput approach for conducting RNA cytometry of individual cells based on their digital gene expression signature.
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Affiliation(s)
- Greta Leonaviciene
- Institute of Biotechnology, Life Sciences Centre, Vilnius University, 7 Sauletekio av., Vilnius, LT-10257, Lithuania
| | - Linas Mazutis
- To whom correspondence should be addressed. Tel: +370 5 2234356;
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14
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Chen D, Nie M, Tang W, Zhang Y, Wang J, Lan Y, Chen Y, Du W. Whole lifecycle observation of single-spore germinated Streptomyces using a nanogap-stabilized microfluidic chip. MLIFE 2022; 1:341-349. [PMID: 38818224 PMCID: PMC10989842 DOI: 10.1002/mlf2.12039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 08/01/2022] [Accepted: 08/12/2022] [Indexed: 06/01/2024]
Abstract
Streptomyces is a model bacterium to study multicellular differentiation and the major reservoir for antibiotics discovery. However, the cellular-level lifecycle of Streptomyces has not been well studied due to its complexity and lack of research tools that can mimic their natural conditions. In this study, we developed a simple microfluidic chip for the cultivation and observation of the entire lifecycle of Streptomyces development from the single-cell perspective. The chip consists of channels for loading samples and supplying nutrients, microwell arrays for the seeding and growth of single spores, and air chambers beside the microwells that facilitate the development of aerial hyphae and spores. A unique feature of this chip is that each microwell is surrounded by a 1.5 µm nanogap connected to an air chamber, which provides a stabilized water-air interface. We used this chip to observe the lifecycle development of Streptomyces coelicolor and Streptomyces griseus germinated from single spores, which revealed differentiation of aerial hyphae with progeny spores at micron-scale water-air interfaces and air chambers. Finally, we demonstrated the applicability of this chip in phenotypic assays by showing that the microbial hormone A-Factor is involved in the regulatory pathways of aerial hyphae and spore formation. The microfluidic chip could become a robust tool for studying multicellular differentiation, single-spore heterogeneity, and secondary metabolism of single-spore germinated Streptomyces.
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Affiliation(s)
- Dongwei Chen
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Mengyue Nie
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of the Chinese Academy of SciencesBeijingChina
| | - Wei Tang
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Yuwei Zhang
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Jian Wang
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Ying Lan
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of the Chinese Academy of SciencesBeijingChina
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- Savaid Medical SchoolUniversity of the Chinese Academy of SciencesBeijingChina
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15
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Yu Y, Wen H, Li S, Cao H, Li X, Ma Z, She X, Zhou L, Huang S. Emerging microfluidic technologies for microbiome research. Front Microbiol 2022; 13:906979. [PMID: 36051769 PMCID: PMC9424851 DOI: 10.3389/fmicb.2022.906979] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
The importance of the microbiome is increasingly prominent. For example, the human microbiome has been proven to be strongly associated with health conditions, while the environmental microbiome is recognized to have a profound influence on agriculture and even the global climate. Furthermore, the microbiome can serve as a fascinating reservoir of genes that encode tremendously valuable compounds for industrial and medical applications. In the past decades, various technologies have been developed to better understand and exploit the microbiome. In particular, microfluidics has demonstrated its strength and prominence in the microbiome research. By taking advantage of microfluidic technologies, inherited shortcomings of traditional methods such as low throughput, labor-consuming, and high-cost are being compensated or bypassed. In this review, we will summarize a broad spectrum of microfluidic technologies that have addressed various needs in the field of microbiome research, as well as the achievements that were enabled by the microfluidics (or technological advances). Finally, how microfluidics overcomes the limitations of conventional methods by technology integration will also be discussed.
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Affiliation(s)
- Yue Yu
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hui Wen
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Sihong Li
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Haojie Cao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xuefei Li
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhixin Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiaoyi She
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Lei Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Shuqiang Huang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Shuqiang Huang,
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16
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Kaari M, Manikkam R, Baskaran A. Exploring Newer Biosynthetic Gene Clusters in Marine Microbial Prospecting. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:448-467. [PMID: 35394575 DOI: 10.1007/s10126-022-10118-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Marine microbes genetically evolved to survive varying salinity, temperature, pH, and other stress factors by producing different bioactive metabolites. These microbial secondary metabolites (SMs) are novel, have high potential, and could be used as lead molecule. Genome sequencing of microbes revealed that they have the capability to produce numerous novel bioactive metabolites than observed under standard in vitro culture conditions. Microbial genome has specific regions responsible for SM assembly, termed biosynthetic gene clusters (BGCs), possessing all the necessary genes to encode different enzymes required to generate SM. In order to augment the microbial chemo diversity and to activate these gene clusters, various tools and techniques are developed. Metagenomics with functional gene expression studies aids in classifying novel peptides and enzymes and also in understanding the biosynthetic pathways. Genome shuffling is a high-throughput screening approach to improve the development of SMs by incorporating genomic recombination. Transcriptionally silent or lower level BGCs can be triggered by artificially knocking promoter of target BGC. Additionally, bioinformatic tools like antiSMASH, ClustScan, NAPDOS, and ClusterFinder are effective in identifying BGCs of existing class for annotation in genomes. This review summarizes the significance of BGCs and the different approaches for detecting and elucidating BGCs from marine microbes.
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Affiliation(s)
- Manigundan Kaari
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India
| | - Radhakrishnan Manikkam
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India.
| | - Abirami Baskaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India
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18
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Davidson SL, Niepa THR. Micro-Technologies for Assessing Microbial Dynamics in Controlled Environments. Front Microbiol 2022; 12:745835. [PMID: 35154021 PMCID: PMC8831547 DOI: 10.3389/fmicb.2021.745835] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
With recent advances in microfabrication technologies, the miniaturization of traditional culturing techniques has provided ideal methods for interrogating microbial communities in a confined and finely controlled environment. Micro-technologies offer high-throughput screening and analysis, reduced experimental time and resources, and have low footprint. More importantly, they provide access to culturing microbes in situ in their natural environments and similarly, offer optical access to real-time dynamics under a microscope. Utilizing micro-technologies for the discovery, isolation and cultivation of "unculturable" species will propel many fields forward; drug discovery, point-of-care diagnostics, and fundamental studies in microbial community behaviors rely on the exploration of novel metabolic pathways. However, micro-technologies are still largely proof-of-concept, and scalability and commercialization of micro-technologies will require increased accessibility to expensive equipment and resources, as well as simpler designs for usability. Here, we discuss three different miniaturized culturing practices; including microarrays, micromachined devices, and microfluidics; advancements to the field, and perceived challenges.
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Affiliation(s)
- Shanna-Leigh Davidson
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, United States
| | - Tagbo H. R. Niepa
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, PA, United States
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, United States
- The McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
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19
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Ye S, Li C, Zheng X, Huang W, Tao Y, Yu Y, Yang L, Lan Y, Ma L, Bian S, Du W. OsciDrop: A Versatile Deterministic Droplet Generator. Anal Chem 2022; 94:2918-2925. [DOI: 10.1021/acs.analchem.1c04852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shun Ye
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Caiming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xu Zheng
- State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China
| | - Weihang Huang
- Department of Linguistics and Modern Languages, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Yi Tao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanghuan Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Limin Yang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Lan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liang Ma
- Dawei Biotechnologies Co., Ltd., Beijing 100085, China
| | - Shengtai Bian
- School of Sport Science, Beijing Sport University, Beijing 100084, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
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20
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Zhu X, Wang K, Yan H, Liu C, Zhu X, Chen B. Microfluidics as an Emerging Platform for Exploring Soil Environmental Processes: A Critical Review. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:711-731. [PMID: 34985862 DOI: 10.1021/acs.est.1c03899] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Investigating environmental processes, especially those occurring in soils, calls for innovative and multidisciplinary technologies that can provide insights at the microscale. The heterogeneity, opacity, and dynamics make the soil a "black box" where interactions and processes are elusive. Recently, microfluidics has emerged as a powerful research platform and experimental tool which can create artificial soil micromodels, enabling exploring soil processes on a chip. Micro/nanofabricated microfluidic devices can mimic some of the key features of soil with highly controlled physical and chemical microenvironments at the scale of pores, aggregates, and microbes. The combination of various techniques makes microfluidics an integrated approach for observation, reaction, analysis, and characterization. In this review, we systematically summarize the emerging applications of microfluidic soil platforms, from investigating soil interfacial processes and soil microbial processes to soil analysis and high-throughput screening. We highlight how innovative microfluidic devices are used to provide new insights into soil processes, mechanisms, and effects at the microscale, which contribute to an integrated interrogation of the soil systems across different scales. Critical discussions of the practical limitations of microfluidic soil platforms and perspectives of future research directions are summarized. We envisage that microfluidics will represent the technological advances toward microscopic, controllable, and in situ soil research.
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Affiliation(s)
- Xiangyu Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Kun Wang
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Huicong Yan
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Congcong Liu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Xiaoying Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Baoliang Chen
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
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21
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Wang F, Li M, Huang L, Zhang XH. Cultivation of uncultured marine microorganisms. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:117-120. [PMID: 37073343 PMCID: PMC10077157 DOI: 10.1007/s42995-021-00093-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 01/11/2021] [Indexed: 05/03/2023]
Affiliation(s)
- Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Oceanography, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060 China
| | - Li Huang
- Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
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