1
|
Jiang X, Peng Z, Zhang J. Starting with screening strains to construct synthetic microbial communities (SynComs) for traditional food fermentation. Food Res Int 2024; 190:114557. [PMID: 38945561 DOI: 10.1016/j.foodres.2024.114557] [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: 03/21/2024] [Revised: 05/16/2024] [Accepted: 05/26/2024] [Indexed: 07/02/2024]
Abstract
With the elucidation of community structures and assembly mechanisms in various fermented foods, core communities that significantly influence or guide fermentation have been pinpointed and used for exogenous restructuring into synthetic microbial communities (SynComs). These SynComs simulate ecological systems or function as adjuncts or substitutes in starters, and their efficacy has been widely verified. However, screening and assembly are still the main limiting factors for implementing theoretic SynComs, as desired strains cannot be effectively obtained and integrated. To expand strain screening methods suitable for SynComs in food fermentation, this review summarizes the recent research trends in using SynComs to study community evolution or interaction and improve the quality of food fermentation, as well as the specific process of constructing synthetic communities. The potential for novel screening modalities based on genes, enzymes and metabolites in food microbial screening is discussed, along with the emphasis on strategies to optimize assembly for facilitating the development of synthetic communities.
Collapse
Affiliation(s)
- Xinyi Jiang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zheng Peng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China.
| |
Collapse
|
2
|
Chen F, Liu K, Shang L, Wang Y, Tang X, Liang P, Li B. Precision isolation and cultivation of single cells by vortex and flat-top laser ejection. Front Microbiol 2024; 15:1369506. [PMID: 38659989 PMCID: PMC11039905 DOI: 10.3389/fmicb.2024.1369506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/19/2024] [Indexed: 04/26/2024] Open
Abstract
Single-cell isolation stands as a critical step in single-cell studies, and single-cell ejection technology based on laser induced forward transfer technology (LIFT) is considered one of the most promising methods in this regard for its ability of visible isolating single cell from complex samples. In this study, we improve the LIFT technology and introduce optical vortex laser-induced forward transfer (OV-LIFT) and flat-top laser-induced forward transfer (FT-LIFT) by utilizing spatial light modulator (SLM), aiming to enhance the precision of single-cell sorting and the cell's viability after ejection. Experimental results demonstrate that applying vortex and flat-top beams during the sorting and collection process enables precise retrieval of single cells within diameter ranges of 50 μm and 100 μm, respectively. The recovery rates of Saccharomyces cerevisiae and Escherichia coli DH5α single cell ejected by vortex beam are 89 and 78%, by flat-top beam are 85 and 57%. When employing Gaussian beam sorting, the receiving range extends to 400 μm, with cultivation success rates of S. cerevisiae and E. coli DH5α single cell are 48 and 19%, respectively. This marks the first application of different mode beams in the ejection and cultivation of single cells, providing a novel and effective approach for the precise isolation and improving the viability of single cells.
Collapse
Affiliation(s)
- Fuyuan Chen
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kunxiang Liu
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lindong Shang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuntong Wang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xusheng Tang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Liang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bei Li
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
3
|
Herzog J, Franke L, Lai Y, Gomez Rossi P, Sachtleben J, Weuster-Botz D. 3D bioprinting of microorganisms: principles and applications. Bioprocess Biosyst Eng 2024; 47:443-461. [PMID: 38296889 PMCID: PMC11003907 DOI: 10.1007/s00449-023-02965-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/24/2023] [Indexed: 02/02/2024]
Abstract
In recent years, the ability to create intricate, live tissues and organs has been made possible thanks to three-dimensional (3D) bioprinting. Although tissue engineering has received a lot of attention, there is growing interest in the use of 3D bioprinting for microorganisms. Microorganisms like bacteria, fungi, and algae, are essential to many industrial bioprocesses, such as bioremediation as well as the manufacture of chemicals, biomaterials, and pharmaceuticals. This review covers current developments in 3D bioprinting methods for microorganisms. We go over the bioink compositions designed to promote microbial viability and growth, taking into account factors like nutrient delivery, oxygen supply, and waste elimination. Additionally, we investigate the most important bioprinting techniques, including extrusion-based, inkjet, and laser-assisted approaches, as well as their suitability with various kinds of microorganisms. We also investigate the possible applications of 3D bioprinted microbes. These range from constructing synthetic microbial consortia for improved metabolic pathway combinations to designing spatially patterned microbial communities for enhanced bioremediation and bioprocessing. We also look at the potential for 3D bioprinting to advance microbial research, including the creation of defined microenvironments to observe microbial behavior. In conclusion, the 3D bioprinting of microorganisms marks a paradigm leap in microbial bioprocess engineering and has the potential to transform many application areas. The ability to design the spatial arrangement of various microorganisms in functional structures offers unprecedented possibilities and ultimately will drive innovation.
Collapse
Affiliation(s)
- Josha Herzog
- Department of Energy and Process Engineering, TUM School of Engineering and Design, Chair of Biochemical Engineering, Technical University of Munich, Boltzmannstraße 15, 85748, Garching, Germany
| | - Lea Franke
- TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Petersgasse 5, 94315, Straubing, Germany
| | - Yingyao Lai
- TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Petersgasse 5, 94315, Straubing, Germany
| | - Pablo Gomez Rossi
- TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Petersgasse 5, 94315, Straubing, Germany
| | - Janina Sachtleben
- TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Petersgasse 5, 94315, Straubing, Germany
| | - Dirk Weuster-Botz
- Department of Energy and Process Engineering, TUM School of Engineering and Design, Chair of Biochemical Engineering, Technical University of Munich, Boltzmannstraße 15, 85748, Garching, Germany.
| |
Collapse
|
4
|
Laser-assisted bioprinting of microorganisms with hydrogel microdroplets: peculiarities of Ascomycota and Basidiomycota yeast transfer. World J Microbiol Biotechnol 2022; 39:29. [PMID: 36437388 DOI: 10.1007/s11274-022-03478-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022]
Abstract
Laser-assisted bioprinting of microbial cells by hydrogel microdroplets is a rapidly developing and promising field that can contribute to solving a number of issues in microbiology and biotechnology. To date, most research on the use of laser bioprinting for microorganism manipulation and sorting has focused on prokaryotes; the bioprinting of eukaryotic microorganisms is much less understood. The use of hydrogel allows solving two fundamental problems: creating comfortable environments for living microorganisms and imparting the necessary rheological properties of the gel for the stable transfer of microdroplets of a preset size. Two main problems were solved in this article. First, the parameters of the hydrogel based on hyaluronic acid and laser fluence to ensure stable transfer of single drops are selected. Second, possible differences in the bioprinting by hyaluronic acid hydrogel microdroplets with yeasts of various taxonomy (Ascomycota vs Basidiomycota), which form and do not form polysaccharide capsules and evaluated. We have performed laser induced forward transfer of 8 yeast species (Goffeauzyma gilvescens, Lipomyces lipofer, Lipomyces starkey, Pichia manshurica, Saitozyma podzolica, Schwanniomyces occidentalis var. occidentalis, Sterigmatosporidium polymorphum, Vanrija humicola) and assessed its viability based on colony formation on the nutrient medium. It is shown that after laser-induced transfer in hydrogel microdroplets the mean viability rate was 77% with some strains showing relatively high viability rates exceeding 90%. Effect of capsules presence on colony formation after laser bioprinting was not revealed. Differences in laser transfer of the yeast of various phyla were found-basidiomycetes formed a greater number of colonies than ascomycetes. The causes and mechanisms of these effects require detailed studies. The data obtained contributes to the knowledge about the bioprinting of eukaryotic microorganisms and can be useful in the studies of single microbial cells and inter-organism interactions.
Collapse
|
5
|
Grosfeld EV, Zhigarkov VS, Alexandrov AI, Minaev NV, Yusupov VI. Theoretical and Experimental Assay of Shock Experienced by Yeast Cells during Laser Bioprinting. Int J Mol Sci 2022; 23:ijms23179823. [PMID: 36077218 PMCID: PMC9456252 DOI: 10.3390/ijms23179823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/17/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Laser-induced forward transfer (LIFT) is a useful technique for bioprinting using gel-embedded cells. However, little is known about the stresses experienced by cells during LIFT. This paper theoretically and experimentally explores the levels of laser pulse irradiation and pulsed heating experienced by yeast cells during LIFT. It has been found that only 5% of the cells in the gel layer adjacent to the absorbing Ti film should be significantly heated for fractions of microseconds, which was confirmed by the fact that a corresponding population of cells died during LIFT. This was accompanied by the near-complete dimming of intracellular green fluorescent protein, also observed in response to heat shock. It is shown that microorganisms in the gel layer experience laser irradiation with an energy density of ~0.1–6 J/cm2. This level of irradiation had no effect on yeast on its own. We conclude that in a wide range of laser fluences, bioprinting kills only a minority of the cell population. Importantly, we detected a previously unobserved change in membrane permeability in viable cells. Our data provide a wider perspective on the effects of LIFT-based bioprinting on living organisms and might provide new uses for the procedure based on its effects on cell permeability.
Collapse
Affiliation(s)
- Erika V. Grosfeld
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the RAS, 119071 Moscow, Russia
- Moscow Institute of Physics and Technology (National Research University), 141700 Dolgoprudny, Russia
- Correspondence: (E.V.G.); (V.I.Y.)
| | - Vyacheslav S. Zhigarkov
- Institute of Photon Technologies of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Pionerskaya 2, Troitsk, 108840 Moscow, Russia
| | - Alexander I. Alexandrov
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the RAS, 119071 Moscow, Russia
| | - Nikita V. Minaev
- Institute of Photon Technologies of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Pionerskaya 2, Troitsk, 108840 Moscow, Russia
| | - Vladimir I. Yusupov
- Institute of Photon Technologies of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Pionerskaya 2, Troitsk, 108840 Moscow, Russia
- Correspondence: (E.V.G.); (V.I.Y.)
| |
Collapse
|
6
|
Isolating and culturing of single microbial cells by laser ejection sorting technology. Appl Environ Microbiol 2021; 88:e0116521. [PMID: 34818099 PMCID: PMC8824209 DOI: 10.1128/aem.01165-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Single cell isolation and cultivation play an important role in studying physiology, gene expression and functions of microorganisms. A series of single-cell isolation technologies have been developed, among which single-cell ejection technology is one of the most promising. Single cell ejection technology has applied Laser Induced Forward Transfer Technique (LIFT) to isolate bacteria but the viability (or recovery rate) of cells after sorting has not been clarified in the current research progress. In this work, to keep the cells alive as much as possible, we propose a three-layer LIFT system (top layer: 25-nm aluminum film; second layer: 3 μm agar media; third layer: liquid containing bacterial) for the isolation and cultivation of single Gram-negative (E. coli), Gram-positive (Lactobacillus rhamnosus GG, LGG), and eukaryotic microorganisms (Saccharomyces cerevisiae). The experiment results showed that the average survival rates for ejected pure single cells were 63% for Saccharomyces cerevisiae, 22% for E. coli DH5α, and 74% for LGG. In addition, we successfully isolated and cultured the GFP expressing E. coli JM109 from the mixture containing complex communities of soil bacteria by fluorescence signal. The average survival rate of E. coli JM109 was demonstrated to be 25.3%. In this study, the isolated and cultured single colonies were further confirmed by colony PCR and sequencing. Such precise sorting and cultivation technique of live single microbial cells could be coupled with other microscopic approaches to isolate single microorganisms with specific functions, revealing their roles in the natural community. Importance We developed a laser induced forward transfer (LIFT) technology to accurately isolate single live microbial cells. The cultivation recovery rates of the ejected single cells were 63% for Saccharomyces cerevisiae, 22% for E. coli DH5α, and 74% for Lactobacillus rhamnosus GG (LGG). Coupled LIFT with fluorescent microscope, we demonstrated that single cells of GFP expressing E. coli JM109 were sorted according to fluorescence signal from a complex community of soil bacteria, and subsequently cultured with 25% cultivation recovery rate. This single cell live sorting technology could isolate single microbes with specific functions, revealing their roles in the natural community.
Collapse
|
7
|
Methods for Studying Bacterial–Fungal Interactions in the Microenvironments of Soil. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11199182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Due to their small size, microorganisms directly experience only a tiny portion of the environmental heterogeneity manifested in the soil. The microscale variations in soil properties constrain the distribution of fungi and bacteria, and the extent to which they can interact with each other, thereby directly influencing their behavior and ecological roles. Thus, to obtain a realistic understanding of bacterial–fungal interactions, the spatiotemporal complexity of their microenvironments must be accounted for. The objective of this review is to further raise awareness of this important aspect and to discuss an overview of possible methodologies, some of easier applicability than others, that can be implemented in the experimental design in this field of research. The experimental design can be rationalized in three different scales, namely reconstructing the physicochemical complexity of the soil matrix, identifying and locating fungi and bacteria to depict their physical interactions, and, lastly, analyzing their molecular environment to describe their activity. In the long term, only relevant experimental data at the cell-to-cell level can provide the base for any solid theory or model that may serve for accurate functional prediction at the ecosystem level. The way to this level of application is still long, but we should all start small.
Collapse
|
8
|
Dou C, Perez V, Qu J, Tsin A, Xu B, Li J. A State‐of‐the‐Art Review of Laser‐Assisted Bioprinting and its Future Research Trends. CHEMBIOENG REVIEWS 2021. [DOI: 10.1002/cben.202000037] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Chaoran Dou
- The University of Texas Rio Grande Valley Department of Manufacturing and Industrial Engineering Edinburg TX USA
| | - Victoria Perez
- The University of Texas Rio Grande Valley Department of Manufacturing and Industrial Engineering Edinburg TX USA
| | - Jie Qu
- The University of Texas Rio Grande Valley Department of Mechanical Engineering Edinburg TX USA
- China University of Mining and Technology School of Electrical and Power Engineering Xuzhou Jiangsu Province China
| | - Andrew Tsin
- The University of Texas Rio Grande Valley School of Medicine Department of Molecular Science USA
| | - Ben Xu
- Mississippi State University Department of Mechanical Engineering Starkville MS USA
| | - Jianzhi Li
- The University of Texas Rio Grande Valley Department of Manufacturing and Industrial Engineering Edinburg TX USA
| |
Collapse
|
9
|
Rumpel C, Ann V, Bahri H, Calabi Floody M, Cheik S, Doan TT, Harit A, Janeau JL, Jouquet P, Mora ML, Podwojewski P, Tran TM, Ngo QA, Rossi PL, Sanaullah M. Research for development in the 21st century. GEODERMA 2020; 378:114558. [PMID: 32836329 DOI: 10.1016/j.geoderma.2020.114588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
- C Rumpel
- CNRS, IRD, Institute of Ecology and Environmental Sciences - Paris, UMR (CNRS, IRD, INRA, Sorbonne University, UPEC), Paris, France
| | - V Ann
- Institute of Technology of Cambodia, Phnom Penh, Cambodia
| | - H Bahri
- Institut National de Recherches en Génie Rural, Eaux et Forêts, Université de Carthage, Tunisia
| | | | - S Cheik
- Gachamaleh, lot 18, 1095 Djibouti, Djibouti
| | - T T Doan
- Soils and Fertilizers Research Institute, Hanoi, Viet Nam
| | - A Harit
- School of Environmental Sciences, Mahatma Gandhi University, Kottayam, India
| | - J L Janeau
- CNRS, IRD, Institute of Ecology and Environmental Sciences - Paris, UMR (CNRS, IRD, INRA, Sorbonne University, UPEC), Paris, France
| | - P Jouquet
- CNRS, IRD, Institute of Ecology and Environmental Sciences - Paris, UMR (CNRS, IRD, INRA, Sorbonne University, UPEC), Paris, France
| | | | - P Podwojewski
- CNRS, IRD, Institute of Ecology and Environmental Sciences - Paris, UMR (CNRS, IRD, INRA, Sorbonne University, UPEC), Paris, France
| | - T M Tran
- Soils and Fertilizers Research Institute, Hanoi, Viet Nam
| | - Q A Ngo
- Institute of Chemistry, VAST, Hanoi, Viet Nam
| | - P L Rossi
- CNRS, IRD, Institute of Ecology and Environmental Sciences - Paris, UMR (CNRS, IRD, INRA, Sorbonne University, UPEC), Paris, France
| | - M Sanaullah
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, Pakistan
| |
Collapse
|
10
|
Duan Q, Lee J. Fast-developing machine learning support complex system research in environmental chemistry. NEW J CHEM 2020. [DOI: 10.1039/c9nj05717j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Machine learning will radically accelerate analysis of complex material networks in environmental chemistry.
Collapse
Affiliation(s)
- Qiannan Duan
- Department of Environment Science
- Shaanxi Normal University
- Xi’an 710062
- China
- State Key Laboratory of Pollution Control and Resource Reuse
| | - Jianchao Lee
- Department of Environment Science
- Shaanxi Normal University
- Xi’an 710062
- China
| |
Collapse
|
11
|
Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA. Genes (Basel) 2019; 10:genes10050325. [PMID: 31035394 PMCID: PMC6562407 DOI: 10.3390/genes10050325] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/19/2019] [Accepted: 04/24/2019] [Indexed: 11/17/2022] Open
Abstract
Despite the recent advancements in culturomics, isolation of the majority of environmental microbiota performing critical ecosystem services, such as bioremediation of contaminants, remains elusive. Towards this end, we conducted a metagenomics-guided comparative assessment of soil microbial diversity and functions present in uraniferous soils relative to those that grew in diffusion chambers (DC) or microbial traps (MT), followed by isolation of uranium (U) resistant microbiota. Shotgun metagenomic analysis performed on the soils used to establish the DC/MT chambers revealed Proteobacterial phyla and Burkholderia genus to be the most abundant among bacteria. The chamber-associated growth conditions further increased their abundances relative to the soils. Ascomycota was the most abundant fungal phylum in the chambers relative to the soils, with Penicillium as the most dominant genus. Metagenomics-based taxonomic findings completely mirrored the taxonomic composition of the retrieved isolates such that the U-resistant bacteria and fungi mainly belonged to Burkholderia and Penicillium species, thus confirming that the chambers facilitated proliferation and subsequent isolation of specific microbiota with environmentally relevant functions. Furthermore, shotgun metagenomic analysis also revealed that the gene classes for carbohydrate metabolism, virulence, and respiration predominated with functions related to stress response, membrane transport, and metabolism of aromatic compounds were also identified, albeit at lower levels. Of major note was the successful isolation of a potentially novel Penicillium species using the MT approach, as evidenced by whole genome sequence analysis and comparative genomic analysis, thus enhancing our overall understanding on the uranium cycling microbiota within the tested uraniferous soils.
Collapse
|
12
|
Gorlenko MV, Chutko EA, Churbanova ES, Minaev NV, Kachesov KI, Lysak LV, Evlashin SA, Cheptsov VS, Rybaltovskiy AO, Yusupov VI, Zhigarkov VS, Davydova GA, Chichkov BN, Bagratashvili VN. Laser MICROSAMPLING of soil microbial community. J Biol Eng 2018; 12:27. [PMID: 30519282 PMCID: PMC6263061 DOI: 10.1186/s13036-018-0117-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 10/31/2018] [Indexed: 01/22/2023] Open
Affiliation(s)
- M V Gorlenko
- 1Department of General Soil Science, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - E A Chutko
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, 142190, Troitsk, Moscow, Russia
| | - E S Churbanova
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, 142190, Troitsk, Moscow, Russia
| | - N V Minaev
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, 142190, Troitsk, Moscow, Russia
| | - K I Kachesov
- 1Department of General Soil Science, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - L V Lysak
- 1Department of General Soil Science, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - S A Evlashin
- 6Center for Design, Manufacturing & Materials, Skolkovo Institute of Science and Technology, 143026, Skolkovo, Moscow, Russia
| | - V S Cheptsov
- 1Department of General Soil Science, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - A O Rybaltovskiy
- 3Institute of Nuclear Physics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - V I Yusupov
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, 142190, Troitsk, Moscow, Russia
| | - V S Zhigarkov
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, 142190, Troitsk, Moscow, Russia
| | - G A Davydova
- 4Institute of Theoretical and Experimental Biophysics RAS, 142290, Puschino, Moscow Branch, Russia
| | - B N Chichkov
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, 142190, Troitsk, Moscow, Russia.,5Leibniz Universität Hannover and Laser Zentrum Hannover e.V, 30419 Hannover, Germany
| | - V N Bagratashvili
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, 142190, Troitsk, Moscow, Russia
| |
Collapse
|
13
|
Cheptsov VS, Churbanova ES, Yusupov VI, Gorlenko MV, Lysak LV, Minaev NV, Bagratashvili VN, Chichkov BN. Laser printing of microbial systems: effect of absorbing metal film. Lett Appl Microbiol 2018; 67:544-549. [PMID: 30223313 DOI: 10.1111/lam.13074] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/24/2018] [Accepted: 09/13/2018] [Indexed: 12/21/2022]
Abstract
Recently, it was shown that laser-induced forward transfer (LIFT) technology and the laser engineering of microbial systems (LEMS) technique (based on LIFT method) are effective for isolation of micro-organisms from different complex substrates. These techniques frequently utilize Au as an absorbing layer material. The purpose of this study was to investigate the influence of absorbing film materials (Au, Ti and Cr) on the effectiveness of laser printing of micro-organisms to improve LEMS and LIFT techniques. It was shown that application of Ti and Cr absorbing layers activates bacterial growth after laser printing and is significantly more effective in comparison to Au films, which actually show a suppressing effect on bacterial cells. Results of this study can be applied for LEMS and LIFT protocols for improving bacterial isolation and microbial growth. SIGNIFICANCE AND IMPACT OF THE STUDY: Laser-induced forward transfer technique (LIFT) is currently used for printing of micro-organisms and in biosensor techniques, for single-cell isolation, and for culturing of micro-organisms from complex substrates. We have studied the influence of absorbing film materials (Au, Ti and Cr) on the effectiveness laser printing of micro-organisms. It was shown that application of Ti and Cr absorbing layers activates bacterial growth and is more effective in LIFT compared to Au films, which actually have a suppressive effect on bacteria cells. The results can improve LIFT protocols for bacteria isolation and culturing of microbial systems.
Collapse
Affiliation(s)
- V S Cheptsov
- Soil Science Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - E S Churbanova
- Institute of Photon Technologies, FSRC "Crystallography and Photonics", RAS, Moscow, Russia
| | - V I Yusupov
- Institute of Photon Technologies, FSRC "Crystallography and Photonics", RAS, Moscow, Russia
| | - M V Gorlenko
- Soil Science Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - L V Lysak
- Soil Science Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - N V Minaev
- Institute of Photon Technologies, FSRC "Crystallography and Photonics", RAS, Moscow, Russia
| | - V N Bagratashvili
- Institute of Photon Technologies, FSRC "Crystallography and Photonics", RAS, Moscow, Russia
| | - B N Chichkov
- Institute of Photon Technologies, FSRC "Crystallography and Photonics", RAS, Moscow, Russia.,Institut für Quantenoptik, Leibniz Universität Hannover, Hannover, Germany
| |
Collapse
|
14
|
Baveye PC, Otten W, Kravchenko A, Balseiro-Romero M, Beckers É, Chalhoub M, Darnault C, Eickhorst T, Garnier P, Hapca S, Kiranyaz S, Monga O, Mueller CW, Nunan N, Pot V, Schlüter S, Schmidt H, Vogel HJ. Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain. Front Microbiol 2018; 9:1929. [PMID: 30210462 PMCID: PMC6119716 DOI: 10.3389/fmicb.2018.01929] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/30/2018] [Indexed: 01/17/2023] Open
Abstract
Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the bulk, macroscopic parameters (e.g., granulometry, pH, soil organic matter, and biomass contents) commonly used to characterize soils provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gasses. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale) that is commensurate with the habitat of many microorganisms. For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. With regard to the microbial aspects, although a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because of the scarcity of relevant experimental data. For significant progress to be made, it is crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead. Fortunately, a number of these challenges may be resolved by brand new measuring equipment that will become commercially available in the very near future.
Collapse
Affiliation(s)
- Philippe C. Baveye
- UMR ECOSYS, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, rance
| | - Wilfred Otten
- School of Water, Energy and Environment, Cranfield University, Cranfield, United Kingdom
| | - Alexandra Kravchenko
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - María Balseiro-Romero
- UMR ECOSYS, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, rance
- Department of Soil Science and Agricultural Chemistry, Centre for Research in Environmental Technologies, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Éléonore Beckers
- Soil–Water–Plant Exchanges, Terra Research Centre, BIOSE, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Maha Chalhoub
- UMR ECOSYS, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - Christophe Darnault
- Laboratory of Hydrogeoscience and Biological Engineering, L.G. Rich Environmental Laboratory, Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, United States
| | - Thilo Eickhorst
- Faculty 2 Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Patricia Garnier
- UMR ECOSYS, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - Simona Hapca
- Dundee Epidemiology and Biostatistics Unit, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Serkan Kiranyaz
- Department of Electrical Engineering, Qatar University, Doha, Qatar
| | - Olivier Monga
- Institut de Recherche pour le Développement, Bondy, France
| | - Carsten W. Mueller
- Lehrstuhl für Bodenkunde, Technical University of Munich, Freising, Germany
| | - Naoise Nunan
- Institute of Ecology and Environmental Sciences – Paris, Sorbonne Universités, CNRS, IRD, INRA, P7, UPEC, Paris, France
| | - Valérie Pot
- UMR ECOSYS, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - Steffen Schlüter
- Soil System Science, Helmholtz-Zentrum für Umweltforschung GmbH – UFZ, Leipzig, Germany
| | - Hannes Schmidt
- Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of Vienna, Vienna, Austria
| | - Hans-Jörg Vogel
- Soil System Science, Helmholtz-Zentrum für Umweltforschung GmbH – UFZ, Leipzig, Germany
- Institute of Soil Science and Plant Nutrition, Martin Luther University of Halle-Wittenberg, Halle, Germany
| |
Collapse
|
15
|
Pröbstel AK, Baranzini SE. The Role of the Gut Microbiome in Multiple Sclerosis Risk and Progression: Towards Characterization of the "MS Microbiome". Neurotherapeutics 2018; 15:126-134. [PMID: 29147991 PMCID: PMC5794700 DOI: 10.1007/s13311-017-0587-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Multiple sclerosis (MS) is the prototypic complex disease, in which both genes and the environment contribute to its pathogenesis. To date, > 200 independent loci across the genome have been associated with MS risk. However, these only explain a fraction of the total phenotypic variance, suggesting the possible presence of additional genetic factors, and, most likely, also environmental factors. New DNA sequencing technologies have enabled the sequencing of all kinds of microorganisms, including those living in and around humans (i.e., microbiomes). The study of bacterial populations inhabiting the gut is of particular interest in autoimmune diseases owing to their key role in shaping immune responses. In this review, we address the potential crosstalk between B cells and the gut microbiota, a relevant scenario in light of recently approved anti-B-cell therapies for MS. In addition, we review recent efforts to characterize the gut microbiome in patients with MS and discuss potential challenges and future opportunities. Finally, we describe the international MS microbiome study, a multicenter effort to study a large population of patients with MS and their healthy household partners to define the core MS microbiome, how it is shaped by disease-modifying therapies, and to explore potential therapeutic interventions.
Collapse
Affiliation(s)
- Anne-Katrin Pröbstel
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Sergio E Baranzini
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, CA, USA.
- Graduate Program in Bioinformatics, University of California, San Francisco, CA, USA.
| |
Collapse
|
16
|
Decesaro A, Machado TS, Cappellaro ÂC, Reinehr CO, Thomé A, Colla LM. Biosurfactants during in situ bioremediation: factors that influence the production and challenges in evalution. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:20831-20843. [PMID: 28815413 DOI: 10.1007/s11356-017-9778-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/14/2017] [Indexed: 06/07/2023]
Abstract
Research on the influence of biosurfactants on the efficiency of in situ bioremediation of contaminated soil is continuously growing. Despite the constant progress in understanding the mechanisms involved in the effects of biosurfactants, there are still many factors that are not sufficiently elucidated. There is a lack of research on autochthonous or exogenous microbial metabolism when biostimulation or bioaugmentation is carried out to produce biosurfactants at contaminated sites. In addition, studies on the application of techniques that measure the biosurfactants produced in situ are needed. This is important because, although the positive influence of biosurfactants is often reported, there are also studies where no effect or negative effects have been observed. This review aimed to examine some studies on factors that can improve the production of biosurfactants in soils during in situ bioremediation. Moreover, this work reviews the methodologies that can be used for measuring the production of these biocomposts. We reviewed studies on the potential of biosurfactants to improve the bioremediation of hydrocarbons, as well as the limitations of methods for the production of these biomolecules by microorganisms in soil.
Collapse
Affiliation(s)
- Andressa Decesaro
- Faculty of Engineering and Architecture, Postgraduate Program in Civil and Environmental Engineering, University of Passo Fundo, Campus I, L1 Building, BR 285, km 171, Zip Code 611, Bairro São José, Passo Fundo, RS, CEP: 99052-900, Brazil
| | - Thaís Strieder Machado
- Faculty of Engineering and Architecture, Postgraduate Program in Civil and Environmental Engineering, University of Passo Fundo, Campus I, L1 Building, BR 285, km 171, Zip Code 611, Bairro São José, Passo Fundo, RS, CEP: 99052-900, Brazil
| | - Ângela Carolina Cappellaro
- Faculty of Engineering and Architecture, Postgraduate Program in Civil and Environmental Engineering, University of Passo Fundo, Campus I, L1 Building, BR 285, km 171, Zip Code 611, Bairro São José, Passo Fundo, RS, CEP: 99052-900, Brazil
| | - Christian Oliveira Reinehr
- Faculty of Engineering and Architecture, Postgraduate Program in Civil and Environmental Engineering, University of Passo Fundo, Campus I, L1 Building, BR 285, km 171, Zip Code 611, Bairro São José, Passo Fundo, RS, CEP: 99052-900, Brazil
| | - Antônio Thomé
- Faculty of Engineering and Architecture, Postgraduate Program in Civil and Environmental Engineering, University of Passo Fundo, Campus I, L1 Building, BR 285, km 171, Zip Code 611, Bairro São José, Passo Fundo, RS, CEP: 99052-900, Brazil
| | - Luciane Maria Colla
- Faculty of Engineering and Architecture, Postgraduate Program in Civil and Environmental Engineering, University of Passo Fundo, Campus I, L1 Building, BR 285, km 171, Zip Code 611, Bairro São José, Passo Fundo, RS, CEP: 99052-900, Brazil.
| |
Collapse
|
17
|
Biniarz P, Łukaszewicz M, Janek T. Screening concepts, characterization and structural analysis of microbial-derived bioactive lipopeptides: a review. Crit Rev Biotechnol 2016; 37:393-410. [PMID: 27098391 DOI: 10.3109/07388551.2016.1163324] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Lipopeptide biosurfactants are surface active biomolecules that are produced by a variety of microorganisms. Microbial lipopeptides have gained the interest of microbiologists, chemists and biochemists for their high biodiversity as well as efficient action, low toxicity and good biodegradability in comparison to synthetic counterparts. In this report, we review methods for the production, isolation and screening, purification and structural characterization of microbial lipopeptides. Several techniques are currently available for each step, and we describe the most commonly utilized and recently developed techniques in this review. Investigations on lipopeptide biosurfactants in natural products require efficient isolation techniques for the characterization and evaluation of chemical and biological properties. A combination of chromatographic and spectroscopic techniques offer opportunities for a better characterization of lipopeptide structures, which in turn can lead to the application of lipopeptides in food, pharmaceutical, cosmetics, agricultural and bioremediation industries.
Collapse
Affiliation(s)
- Piotr Biniarz
- a Faculty of Biotechnology, University of Wroclaw , Wroclaw, Poland
| | | | - Tomasz Janek
- a Faculty of Biotechnology, University of Wroclaw , Wroclaw, Poland.,b Department of Inorganic Chemistry, Faculty of Pharmacy, Wroclaw Medical University , Wroclaw, Poland
| |
Collapse
|