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Gorniak L, Bucka SL, Nasr B, Cao J, Hellmann S, Schäfer T, Westermann M, Bechwar J, Wegner CE. Changes in growth, lanthanide binding, and gene expression in Pseudomonas alloputida KT2440 in response to light and heavy lanthanides. mSphere 2024:e0068524. [PMID: 39291981 DOI: 10.1128/msphere.00685-24] [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: 08/13/2024] [Accepted: 08/16/2024] [Indexed: 09/19/2024] Open
Abstract
Pseudomonas alloputida KT2440 is a ubiquitous, soil-dwelling bacterium that metabolizes recalcitrant and volatile carbon sources. The latter is utilized by two redundant, Ca- and lanthanide (Ln)-dependent, pyrroloquinoline quinone-dependent alcohol dehydrogenases (PQQ ADH), PedE and PedH, whose expression is regulated by Ln availability. P. alloputida KT2440 is the best-studied non-methylotroph in the context of Ln-utilization. Combined with microfluidic cultivation and single-cell elemental analysis, we studied the impact of light and heavy Ln on transcriptome-wide gene expression when growing P. alloputida KT2440 with 2-phenylethanol as the carbon and energy source. Light Ln (La, Ce, and Nd) and a mixture of light and heavy Ln (La, Ce, Nd, Dy, Ho, Er, and Yb) had a positive effect on growth, whereas supplementation with heavy Ln (Dy, Ho, Er, and Yb) exerted fitness costs. These were likely a consequence of mismetallation and non-utilizable Ln interfering with Ln sensing and signaling. The measured amounts of cell-associated Ln varied between elements. Gene expression analysis suggested that the Ln sensing and signaling machinery, the two-component system PedS2R2 and PedH, responds differently to (non-)utilizable Ln. We expanded our understanding of the lanthanide (Ln) switch in P. alloputida KT2440, demonstrating that it adjusts the levels of pedE and pedH transcripts based on the availability of Ln. We propose that the usability of Ln influences the bacterium's response to different Ln elements.IMPORTANCEThe Ln switch, the inverse regulation of Ca- and Ln-dependent PQQ ADH in response to Ln availability in organisms featuring both, is central to our understanding of Ln utilization. Although the preference of bacteria for light Ln is well known, the effect of different Ln, light and heavy, on growth and gene expression has rarely been studied. We provide evidence for a fine-tuning mechanism of Ca- and Ln-dependent PQQ ADH in P. alloputida KT2440 on the transcriptome level. The response to (non-)utilizable Ln differs depending on the element. Ln commonly co-occur in nature. Our findings underline that Ln-utilizing microbes must be able to discriminate between Ln to use them effectively. Considering the prevalence of Ln-dependent proteins in many microbial taxa, more work addressing Ln sensing and signaling is needed. Ln availability likely necessitates different adaptations regarding Ln utilization.
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Affiliation(s)
- Linda Gorniak
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Jena, Germany
| | - Sarah Luise Bucka
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Jena, Germany
| | - Bayan Nasr
- Department of Physical Chemistry and Microreaction Technology, Institute for Chemistry and Biotechnique, Technische Universität Ilmenau, Ilmenau, Germany
| | - Jialan Cao
- Department of Physical Chemistry and Microreaction Technology, Institute for Chemistry and Biotechnique, Technische Universität Ilmenau, Ilmenau, Germany
| | - Steffen Hellmann
- Institute of Geosciences, Applied Geology, Friedrich Schiller University Jena, Jena, Germany
- International Max Planck Research School for Global Biogeochemical Cycles, Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Thorsten Schäfer
- Institute of Geosciences, Applied Geology, Friedrich Schiller University Jena, Jena, Germany
| | | | - Julia Bechwar
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Jena, Germany
| | - Carl-Eric Wegner
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Jena, Germany
- Bioinorganic Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Richter F, Chen M, Schaub P, Wüst F, Zhang D, Schneider S, Groß GA, Mäder P, Dovzhenko O, Palme K, Köhler JM, Cao J. Induction of embryogenic development in haploid microspore stem cells in droplet-based microfluidics. LAB ON A CHIP 2022; 22:4292-4305. [PMID: 36196753 DOI: 10.1039/d2lc00788f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
This work presents the application of droplet-based microfluidics for the cultivation of microspores from Brassica napus using the doubled haploid technology. Under stress conditions (e.g. heat shock) or by chemical induction a certain fraction of the microspores can be reprogrammed and androgenesis can be induced. This process is an important approach for plant breeding because desired plant properties can be anchored in the germline on a genetic level. However, the reprogramming rate of the microspores is generally very low, increasing it by specific stimulation is, therefore, both a necessary and challenging task. In order to accelerate the optimisation and development process, the application of droplet-based microfluidics can be a promising tool. Here, we used a tube-based microfluidic system for the generation and cultivation of microspores inside nL-droplets. Different factors like cell density, tube material and heat shock conditions were investigated to improve the yield of vital plant organoids. Evaluation and analysis of the stimuli response were done on an image base aided by an artificial intelligence cell detection algorithm. Droplet-based microfluidics allowed us to apply large concentration programs in small test volumes and to screen the best conditions for reprogramming cells by the histone deacetylase inhibitor trichostatin A and for enhancing the yield of vital microspores in droplets. An enhanced reprogramming rate was found under the heat shock conditions at 32 °C for about 3 to 6 days. In addition, the comparative experiment with MTP showed that droplet cultivation with lower cell density (<10 cells per droplet) or adding media after 3 or 6 days significantly positively affects the microspore growth and embryo rate inside 120 nL droplets. Finally, the developed embryos could be removed from the droplets and further grown into mature plants. Overall, we demonstrated that the droplet-based tube system is suitable for implementation in an automated, miniaturized system to achieve the induction of embryogenic development in haploid microspore stem cells of Brassica napus.
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Affiliation(s)
- Felix Richter
- Institute for Chemistry and Biotechnologies, Dept. Physical Chemistry and Microreaction Technologies, Technische Universität Ilmenau, 98693 Ilmenau, Germany.
| | - Minqian Chen
- Technische Universität Ilmenau, Institute for Computer and Systems Engineering, Dept. Software Engineering for Safety-Critical Systems, 98693 Ilmenau, Germany
| | | | - Florian Wüst
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University of Freiburg, 79104 Freiburg, Germany
| | - Di Zhang
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University of Freiburg, 79104 Freiburg, Germany
| | - Steffen Schneider
- Institute for Chemistry and Biotechnologies, Dept. Physical Chemistry and Microreaction Technologies, Technische Universität Ilmenau, 98693 Ilmenau, Germany.
| | - G Alexander Groß
- Institute for Chemistry and Biotechnologies, Dept. Physical Chemistry and Microreaction Technologies, Technische Universität Ilmenau, 98693 Ilmenau, Germany.
| | - Patrick Mäder
- Technische Universität Ilmenau, Institute for Computer and Systems Engineering, Dept. Software Engineering for Safety-Critical Systems, 98693 Ilmenau, Germany
| | | | - Klaus Palme
- ScreenSYS GmbH, 79104 Freiburg, Germany
- Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University of Freiburg, 79104 Freiburg, Germany
- BIOSS Centre of Biological Signalling Studies, Albert-Ludwigs-University of Freiburg, 79104 Freiburg, Germany
- Sino-German Joint Research Center on Agricultural Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China
| | - J Michael Köhler
- Institute for Chemistry and Biotechnologies, Dept. Physical Chemistry and Microreaction Technologies, Technische Universität Ilmenau, 98693 Ilmenau, Germany.
| | - Jialan Cao
- Institute for Chemistry and Biotechnologies, Dept. Physical Chemistry and Microreaction Technologies, Technische Universität Ilmenau, 98693 Ilmenau, Germany.
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Cao J, Russo DA, Xie T, Groß GA, Zedler JAZ. A droplet-based microfluidic platform enables high-throughput combinatorial optimization of cyanobacterial cultivation. Sci Rep 2022; 12:15536. [PMID: 36109626 PMCID: PMC9477827 DOI: 10.1038/s41598-022-19773-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/05/2022] [Indexed: 11/09/2022] Open
Abstract
Cyanobacteria are fast-growing, genetically accessible, photoautotrophs. Therefore, they have attracted interest as sustainable production platforms. However, the lack of techniques to systematically optimize cultivation parameters in a high-throughput manner is holding back progress towards industrialization. To overcome this bottleneck, here we introduce a droplet-based microfluidic platform capable of one- (1D) and two-dimension (2D) screening of key parameters in cyanobacterial cultivation. We successfully grew three different unicellular, biotechnologically relevant, cyanobacteria: Synechocystis sp. PCC 6803, Synechococcus elongatus UTEX 2973 and Synechococcus sp. UTEX 3154. This was followed by a highly-resolved 1D screening of nitrate, phosphate, carbonate, and salt concentrations. The 1D screening results suggested that nitrate and/or phosphate may be limiting nutrients in standard cultivation media. Finally, we use 2D screening to determine the optimal N:P ratio of BG-11. Application of the improved medium composition in a high-density cultivation setup led to an increase in biomass yield of up to 15.7%. This study demonstrates that droplet-based microfluidics can decrease the volume required for cyanobacterial cultivation and screening up to a thousand times while significantly increasing the multiplexing capacity. Going forward, microfluidics have the potential to play a significant role in the industrial exploitation of cyanobacteria.
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Cao J, Chande C, Köhler JM. Microtoxicology by microfluidic instrumentation: a review. LAB ON A CHIP 2022; 22:2600-2623. [PMID: 35678285 DOI: 10.1039/d2lc00268j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Microtoxicology is concerned with the toxic effects of small amounts of substances. This review paper discusses the application of small amounts of noxious substances for toxicological investigation in small volumes. The vigorous development of miniaturized methods in microfluidics over the last two decades involves chip-based devices, micro droplet-based procedures, and the use of micro-segmented flow for microtoxicological studies. The studies have shown that the microfluidic approach is particularly valuable for highly parallelized and combinatorial dose-response screenings. Accurate dosing and mixing of effector substances in large numbers of microcompartments supplies detailed data of dose-response functions by highly concentration-resolved assays and allows evaluation of stochastic responses in case of small separated cell ensembles and single cell experiments. The investigations demonstrate that very different biological targets can be studied using miniaturized approaches, among them bacteria, eukaryotic microorganisms, cell cultures from tissues of multicellular organisms, stem cells, and early embryonic states. Cultivation and effector exposure tests can be performed in small volumes over weeks and months, confirming that the microfluicial strategy is also applicable for slow-growing organisms. Here, the state of the art of miniaturized toxicology, particularly for studying antibiotic susceptibility, drug toxicity testing in the miniaturized system like organ-on-chip, environmental toxicology, and the characterization of combinatorial effects by two and multi-dimensional screenings, is discussed. Additionally, this review points out the practical limitations of the microtoxicology platform and discusses perspectives on future opportunities and challenges.
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Affiliation(s)
- Jialan Cao
- Techn. Univ. Ilmenau, Dept. Phys. Chem. and Microreaction Technology, Institute for Micro- und Nanotechnologies/Institute for Chemistry and Biotechnology, Ilmenau, Germany.
| | - Charmi Chande
- Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| | - J Michael Köhler
- Techn. Univ. Ilmenau, Dept. Phys. Chem. and Microreaction Technology, Institute for Micro- und Nanotechnologies/Institute for Chemistry and Biotechnology, Ilmenau, Germany.
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Henkel T, Mayer G, Hampl J, Cao J, Ehrhardt L, Schober A, Groß GA. From Microtiter Plates to Droplets—There and Back Again. MICROMACHINES 2022; 13:mi13071022. [PMID: 35888839 PMCID: PMC9316479 DOI: 10.3390/mi13071022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 02/05/2023]
Abstract
Droplet-based microfluidic screening techniques can benefit from interfacing established microtiter plate-based screening and sample management workflows. Interfacing tools are required both for loading preconfigured microtiter-plate (MTP)-based sample collections into droplets and for dispensing the used droplets samples back into MTPs for subsequent storage or further processing. Here, we present a collection of Digital Microfluidic Pipetting Tips (DMPTs) with integrated facilities for droplet generation and manipulation together with a robotic system for its operation. This combination serves as a bidirectional sampling interface for sample transfer from wells into droplets (w2d) and vice versa droplets into wells (d2w). The DMPT were designed to fit into 96-deep-well MTPs and prepared from glass by means of microsystems technology. The aspirated samples are converted into the channel-confined droplets’ sequences separated by an immiscible carrier medium. To comply with the demands of dose-response assays, up to three additional assay compound solutions can be added to the sample droplets. To enable different procedural assay protocols, four different DMPT variants were made. In this way, droplet series with gradually changing composition can be generated for, e.g., 2D screening purposes. The developed DMPT and their common fluidic connector are described here. To handle the opposite transfer d2w, a robotic transfer system was set up and is described briefly.
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Affiliation(s)
- Thomas Henkel
- Leibniz Institute of Photonic Technology, Leibniz-IPHT, Albert-Einstein-Str. 9, 07745 Jena, Germany; (T.H.); (G.M.)
| | - Günter Mayer
- Leibniz Institute of Photonic Technology, Leibniz-IPHT, Albert-Einstein-Str. 9, 07745 Jena, Germany; (T.H.); (G.M.)
| | - Jörg Hampl
- Department of Nano-Biosystem Technology, Institute of Chemistry and Biotechnology, Technical University Ilmenau, Prof.-Schmidt-Str. 26, 98693 Ilmenau, Germany; (J.H.); (A.S.)
| | - Jialan Cao
- Department of Physical Chemistry and Microreaction Technologies, Institute of Chemistry and Biotechnology, Technical University Ilmenau, Prof.-Schmidt-Str. 26, 98693 Ilmenau, Germany; (J.C.); (L.E.)
| | - Linda Ehrhardt
- Department of Physical Chemistry and Microreaction Technologies, Institute of Chemistry and Biotechnology, Technical University Ilmenau, Prof.-Schmidt-Str. 26, 98693 Ilmenau, Germany; (J.C.); (L.E.)
| | - Andreas Schober
- Department of Nano-Biosystem Technology, Institute of Chemistry and Biotechnology, Technical University Ilmenau, Prof.-Schmidt-Str. 26, 98693 Ilmenau, Germany; (J.H.); (A.S.)
| | - Gregor Alexander Groß
- Department of Physical Chemistry and Microreaction Technologies, Institute of Chemistry and Biotechnology, Technical University Ilmenau, Prof.-Schmidt-Str. 26, 98693 Ilmenau, Germany; (J.C.); (L.E.)
- Correspondence: ; Tel.: +49-3677-69-3716
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