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de Pins B, Greenspoon L, Bar-On YM, Shamshoum M, Ben-Nissan R, Milshtein E, Davidi D, Sharon I, Mueller-Cajar O, Noor E, Milo R. A systematic exploration of bacterial form I rubisco maximal carboxylation rates. EMBO J 2024:10.1038/s44318-024-00119-z. [PMID: 38806660 DOI: 10.1038/s44318-024-00119-z] [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: 02/01/2024] [Revised: 03/26/2024] [Accepted: 04/22/2024] [Indexed: 05/30/2024] Open
Abstract
Autotrophy is the basis for complex life on Earth. Central to this process is rubisco-the enzyme that catalyzes almost all carbon fixation on the planet. Yet, with only a small fraction of rubisco diversity kinetically characterized so far, the underlying biological factors driving the evolution of fast rubiscos in nature remain unclear. We conducted a high-throughput kinetic characterization of over 100 bacterial form I rubiscos, the most ubiquitous group of rubisco sequences in nature, to uncover the determinants of rubisco's carboxylation velocity. We show that the presence of a carboxysome CO2 concentrating mechanism correlates with faster rubiscos with a median fivefold higher rate. In contrast to prior studies, we find that rubiscos originating from α-cyanobacteria exhibit the highest carboxylation rates among form I enzymes (≈10 s-1 median versus <7 s-1 in other groups). Our study systematically reveals biological and environmental properties associated with kinetic variation across rubiscos from nature.
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Affiliation(s)
- Benoit de Pins
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Lior Greenspoon
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yinon M Bar-On
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Melina Shamshoum
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Roee Ben-Nissan
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Eliya Milshtein
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Dan Davidi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
- Aleph, Tel Aviv-Yafo, 6688210, Israel
| | - Itai Sharon
- Migal Galilee Research Institute, Kiryat Shmona, 11016, Israel
| | - Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel.
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2
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Secaira-Morocho H, Chede A, Gonzalez-de-Salceda L, Garcia-Pichel F, Zhu Q. An evolutionary optimum amid moderate heritability in prokaryotic cell size. Cell Rep 2024; 43:114268. [PMID: 38776226 DOI: 10.1016/j.celrep.2024.114268] [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: 01/04/2024] [Revised: 04/11/2024] [Accepted: 05/08/2024] [Indexed: 05/24/2024] Open
Abstract
We investigate the distribution and evolution of prokaryotic cell size based on a compilation of 5,380 species. Size spans four orders of magnitude, from 100 nm (Mycoplasma) to more than 1 cm (Thiomargarita); however, most species congregate heavily around the mean. The distribution approximates but is distinct from log normality. Comparative phylogenetics suggests that size is heritable, yet the phylogenetic signal is moderate, and the degree of heritability is independent of taxonomic scale (i.e., fractal). Evolutionary modeling indicates the presence of an optimal cell size to which most species gravitate. The size is equivalent to a coccus of 0.70 μm in diameter. Analyses of 1,361 species with sequenced genomes show that genomic traits contribute to size evolution moderately and synergistically. Given our results, scaling theory, and empirical evidence, we discuss potential drivers that may expand or shrink cells around the optimum and propose a stability landscape model for prokaryotic cell size.
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Affiliation(s)
- Henry Secaira-Morocho
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Abhinav Chede
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Luis Gonzalez-de-Salceda
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Ferran Garcia-Pichel
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Qiyun Zhu
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
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Ale Enriquez F, Ahring BK. Phenotypic and genomic characterization of Methanothermobacter wolfeii strain BSEL, a CO 2-capturing archaeon with minimal nutrient requirements. Appl Environ Microbiol 2024; 90:e0026824. [PMID: 38619268 PMCID: PMC11107166 DOI: 10.1128/aem.00268-24] [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: 02/14/2024] [Accepted: 03/17/2024] [Indexed: 04/16/2024] Open
Abstract
A new variant of Methanothermobacter wolfeii was isolated from an anaerobic digester using enrichment cultivation in anaerobic conditions. The new isolate was taxonomically identified via 16S rRNA gene sequencing and tagged as M. wolfeii BSEL. The whole genome of the new variant was sequenced and de novo assembled. Genomic variations between the BSEL strain and the type strain were discovered, suggesting evolutionary adaptations of the BSEL strain that conferred advantages while growing under a low concentration of nutrients. M. wolfeii BSEL displayed the highest specific growth rate ever reported for the wolfeii species (0.27 ± 0.03 h-1) using carbon dioxide (CO2) as unique carbon source and hydrogen (H2) as electron donor. M. wolfeii BSEL grew at this rate in an environment with ammonium (NH4+) as sole nitrogen source. The minerals content required to cultivate the BSEL strain was relatively low and resembled the ionic background of tap water without mineral supplements. Optimum growth rate for the new isolate was observed at 64°C and pH 8.3. In this work, it was shown that wastewater from a wastewater treatment facility can be used as a low-cost alternative medium to cultivate M. wolfeii BSEL. Continuous gas fermentation fed with a synthetic biogas mimic along with H2 in a bubble column bioreactor using M. wolfeii BSEL as biocatalyst resulted in a CO2 conversion efficiency of 97% and a final methane (CH4) titer of 98.5%v, demonstrating the ability of the new strain for upgrading biogas to renewable natural gas.IMPORTANCEAs a methanogenic archaeon, Methanothermobacter wolfeii uses CO2 as electron acceptor, producing CH4 as final product. The metabolism of M. wolfeii can be harnessed to capture CO2 from industrial emissions, besides producing a drop-in renewable biofuel to substitute fossil natural gas. If used as biocatalyst in new-generation CO2 sequestration processes, M. wolfeii has the potential to accelerate the decarbonization of the energy generation sector, which is the biggest contributor of CO2 emissions worldwide. Nonetheless, the development of CO2 sequestration archaeal-based biotechnology is still limited by an uncertainty in the requirements to cultivate methanogenic archaea and the unknown longevity of archaeal cultures. In this study, we report the adaptation, isolation, and phenotypic characterization of a novel variant of M. wolfeii, which is capable of maximum growth with minimal nutrients input. Our findings demonstrate the potential of this variant for the production of renewable natural gas, paving the way for the development of more efficient and sustainable CO2 sequestration processes.
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Affiliation(s)
- Fuad Ale Enriquez
- Bioproducts, Sciences, and Engineering Laboratory, Washington State University, Tri-Cities, Richland, Washington, USA
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, USA
| | - Birgitte K. Ahring
- Bioproducts, Sciences, and Engineering Laboratory, Washington State University, Tri-Cities, Richland, Washington, USA
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, USA
- Biological Systems Engineering Department, Washington State University, Pullman, Washington, USA
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4
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Boutillon A, Banavar SP, Campàs O. Conserved physical mechanisms of cell and tissue elongation. Development 2024; 151:dev202687. [PMID: 38767601 DOI: 10.1242/dev.202687] [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] [Indexed: 05/22/2024]
Abstract
Living organisms have the ability to self-shape into complex structures appropriate for their function. The genetic and molecular mechanisms that enable cells to do this have been extensively studied in several model and non-model organisms. In contrast, the physical mechanisms that shape cells and tissues have only recently started to emerge, in part thanks to new quantitative in vivo measurements of the physical quantities guiding morphogenesis. These data, combined with indirect inferences of physical characteristics, are starting to reveal similarities in the physical mechanisms underlying morphogenesis across different organisms. Here, we review how physics contributes to shape cells and tissues in a simple, yet ubiquitous, morphogenetic transformation: elongation. Drawing from observed similarities across species, we propose the existence of conserved physical mechanisms of morphogenesis.
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Affiliation(s)
- Arthur Boutillon
- Cluster of Excellence Physics of Life, TU Dresden, 01062 Dresden, Germany
| | - Samhita P Banavar
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540, USA
| | - Otger Campàs
- Cluster of Excellence Physics of Life, TU Dresden, 01062 Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Center for Systems Biology Dresden, 01307 Dresden, Germany
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5
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Sadowska M, Nattich-Rak M, Morga M, Adamczyk Z, Basinska T, Mickiewicz D, Gadzinowski M. Anisotropic Particle Deposition Kinetics from Quartz Crystal Microbalance Measurements: Beyond the Sphere Paradigm. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:7907-7919. [PMID: 38578865 PMCID: PMC11025136 DOI: 10.1021/acs.langmuir.3c03676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 04/07/2024]
Abstract
Deposition kinetics of polymer particles characterized by a prolate spheroid shape on gold sensors modified by the adsorption of poly(allylamine) was investigated using a quartz crystal microbalance and atomic force microscopy. Reference measurements were also performed for polymer particles of a spherical shape and the same diameter as the spheroid shorter axis. Primarily, the frequency and dissipation shifts for various overtones were measured as a function of time. These kinetic data were transformed into the dependence of the complex impedance, scaled up by the inertia impedance, upon the particle size to the hydrodynamic boundary layer ratio. The results obtained for low particle coverage were interpolated, which enabled the derivation of Sauerbrey-like equations, yielding the real particle coverage using the experimental frequency or dissipation (bandwidth) shifts. Experiments carried out for a long deposition time confirmed that, for spheroids, the imaginary and real impedance components were equal to each other for all overtones and for a large range of particle coverage. This result was explained in terms of a hydrodynamic, lubrication-like contact of particles with the sensor, enabling their sliding motion. In contrast, the experimental data obtained for spheres, where the impedance ratio was a complicated function of overtones and particle coverage, showed that the contact was rather stiff, preventing their motion over the sensor. It was concluded that results obtained in this work can be exploited as useful reference systems for a quantitative interpretation of bioparticle, especially bacteria, deposition kinetics on macroion-modified surfaces.
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Affiliation(s)
- Marta Sadowska
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Małgorzata Nattich-Rak
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Maria Morga
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Zbigniew Adamczyk
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Teresa Basinska
- Centre
of Molecular and Macromolecular Studies, Polish Academy of Sciences, Henryka Sienkiewicza 112, 90-363 Lodz, Poland
| | - Damian Mickiewicz
- Centre
of Molecular and Macromolecular Studies, Polish Academy of Sciences, Henryka Sienkiewicza 112, 90-363 Lodz, Poland
| | - Mariusz Gadzinowski
- Centre
of Molecular and Macromolecular Studies, Polish Academy of Sciences, Henryka Sienkiewicza 112, 90-363 Lodz, Poland
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Harlé O, Niay J, Parayre S, Nicolas A, Henry G, Maillard MB, Valence F, Thierry A, Guédon É, Falentin H, Deutsch SM. Deciphering the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during soy juice fermentation using phenotypic and transcriptional analysis. Appl Environ Microbiol 2024; 90:e0193623. [PMID: 38376234 PMCID: PMC10952386 DOI: 10.1128/aem.01936-23] [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: 11/10/2023] [Accepted: 01/03/2024] [Indexed: 02/21/2024] Open
Abstract
In the context of sustainable diet, the development of soy-based yogurt fermented with lactic acid bacteria is an attractive alternative to dairy yogurts. To decipher the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during soy juice (SJ) fermentation, the whole genome of the strain CIRM-BIA865 (Ld865) was sequenced and annotated. Then Ld865 was used to ferment SJ. Samples were analyzed throughout fermentation for their cell number, carbohydrate, organic acid, free amino acid, and volatile compound contents. Despite acidification, the number of Ld865 cells did not rise, and microscopic observations revealed the elongation of cells from 3.6 µm (inoculation) to 36.9 µm (end of fermentation). This elongation was observed in SJ but not in laboratory-rich medium MRS. Using transcriptomic analysis, we showed that the biosynthesis genes of peptidoglycan and membrane lipids were stably expressed, in line with the cell elongation observed, whereas no genes implicated in cell division were upregulated. Among the main sugars available in SJ (sucrose, raffinose, and stachyose), Ld865 only used sucrose. The transcriptomic analysis showed that Ld865 implemented the two transport systems that it contains to import sucrose: a PTS system and an ABC transporter. To fulfill its nitrogen needs, Ld865 probably first consumed the free amino acids of the SJ and then implemented different oligopeptide transporters and proteolytic/peptidase enzymes. In conclusion, this study showed that Ld865 enables fast acidification of SJ, despite the absence of cell division, leads to a product rich in free amino acids, and also leads to the production of aromatic compounds of interest. IMPORTANCE To reduce the environmental and health concerns related to food, an alternative diet is recommended, containing 50% of plant-based proteins. Soy juice, which is protein rich, is a relevant alternative to animal milk, for the production of yogurt-like products. However, soy "beany" and "green" off-flavors limit the consumption of such products. The lactic acid bacteria (LAB) used for fermentation can help to improve the organoleptic properties of soy products. But metabolic data concerning LAB adapted to soy juice are lacking. The aim of this study was, thus, to decipher the metabolism of Lactobacillus delbrueckii subsp. delbrueckii during fermentation of a soy juice, based on a multidisciplinary approach. This result will contribute to give tracks for a relevant selection of starter. Indeed, the improvement of the organoleptic properties of these types of products could help to promote plant-based proteins in our diet.
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Affiliation(s)
- Olivier Harlé
- INRAE, Institut Agro, STLO, Rennes, France
- Olga-Triballat Noyal, R&D UF, Noyal-sur-Vilaine, France
| | - Jérôme Niay
- Olga-Triballat Noyal, R&D UF, Noyal-sur-Vilaine, France
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7
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Ouyang P, Yang J, Zhong Q, Yuan Y, Gao Y, Wang H, Yang ST. Toxicity of VO 2 micro/nanoparticles to nitrogen-fixing bacterium Azotobacter vinelandii. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133553. [PMID: 38266589 DOI: 10.1016/j.jhazmat.2024.133553] [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: 08/25/2023] [Revised: 01/06/2024] [Accepted: 01/16/2024] [Indexed: 01/26/2024]
Abstract
Vanadium dioxide (VO2) has been used in a variety of products due to its outstanding phase transition properties. However, as potential heavy metal contaminants, the environmental hazards and risks of VO2 should be systematically investigated. Biological nitrogen fixation is one of the most dominant processes in biogeochemical cycle, which is associated with nitrogen-fixing bacteria. In this study, we reported the environmental bio-effects of VO2 micro/nanoparticles on the nitrogen-fixing bacterium Azotobacter vinelandii. VO2 at 10 and 30 mg/L caused severe hazards to A. vinelandii, such as cell apoptosis, oxidative damage, physical damage, genotoxicity, and the loss of nitrogen fixation activity. The up-regulated differentially expressed genes of A. vinelandii were related to stress response, and the down-regulated genes were mainly related to energy metabolism. Surprisingly, VO2 of 10 mg/L decreased the nif gene expression but elevated the vnf gene expression, which enhanced the ability of A. vinelandii to reduce acetylene in anaerobic environment. In addition, under tested conditions, VO2 nanoparticles exhibited insignificantly higher toxicity than VO2 microparticles.
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Affiliation(s)
- Peng Ouyang
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China; College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Jinwei Yang
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
| | - Qinmei Zhong
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
| | - Yue Yuan
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
| | - Yanfeng Gao
- School of Materials Science and Engineering, Shanghai University, Shanghai 200444, China
| | - Haifang Wang
- Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 200444, China.
| | - Sheng-Tao Yang
- Key Laboratory of Pollution Control Chemistry and Environmental Functional Materials for Qinghai-Tibet Plateau of the National Ethnic Affairs Commission, Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, School of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China.
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8
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ElGamel M, Mugler A. Effects of Molecular Noise on Cell Size Control. PHYSICAL REVIEW LETTERS 2024; 132:098403. [PMID: 38489620 DOI: 10.1103/physrevlett.132.098403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024]
Abstract
Cells employ control strategies to maintain a stable size. Dividing at a target size (the "sizer" strategy) is thought to produce the tightest size distribution. However, this result follows from phenomenological models that ignore the molecular mechanisms required to implement the strategy. Here we investigate a simple mechanistic model for exponentially growing cells whose division is triggered at a molecular abundance threshold. We find that size noise inherits the molecular noise and is consequently minimized not by the sizer but by the "adder" strategy, where a cell divides after adding a target amount to its birth size. We derive a lower bound on size noise that agrees with publicly available data from six microfluidic studies on Escherichia coli bacteria.
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Affiliation(s)
- Motasem ElGamel
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Andrew Mugler
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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Soni J, Sinha S, Pandey R. Understanding bacterial pathogenicity: a closer look at the journey of harmful microbes. Front Microbiol 2024; 15:1370818. [PMID: 38444801 PMCID: PMC10912505 DOI: 10.3389/fmicb.2024.1370818] [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: 01/15/2024] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Abstract
Bacteria are the most prevalent form of microorganisms and are classified into two categories based on their mode of existence: intracellular and extracellular. While most bacteria are beneficial to human health, others are pathogenic and can cause mild to severe infections. These bacteria use various mechanisms to evade host immunity and cause diseases in humans. The susceptibility of a host to bacterial infection depends on the effectiveness of the immune system, overall health, and genetic factors. Malnutrition, chronic illnesses, and age-related vulnerabilities are the additional confounders to disease severity phenotypes. The impact of bacterial pathogens on public health includes the transmission of these pathogens from healthcare facilities, which contributes to increased morbidity and mortality. To identify the most significant threats to public health, it is crucial to understand the global burden of common bacterial pathogens and their pathogenicity. This knowledge is required to improve immunization rates, improve the effectiveness of vaccines, and consider the impact of antimicrobial resistance when assessing the situation. Many bacteria have developed antimicrobial resistance, which has significant implications for infectious diseases and favors the survival of resilient microorganisms. This review emphasizes the significance of understanding the bacterial pathogens that cause this health threat on a global scale.
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Affiliation(s)
- Jyoti Soni
- Division of Immunology and Infectious Disease Biology, Integrative Genomics of Host Pathogen Laboratory, Council of Scientific & Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Sristi Sinha
- Division of Immunology and Infectious Disease Biology, Integrative Genomics of Host Pathogen Laboratory, Council of Scientific & Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
- School of Biosciences and Technology, Vellore Institute of Technology University, Vellore, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, Integrative Genomics of Host Pathogen Laboratory, Council of Scientific & Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
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10
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Chen L, Low HR, Jiang Y, Zhang WY, Ao CK, Tan YJN, Lim KH, Soh S. Functional polymeric molecules for performing autonomous synthesis of particles with core-shell structures and customizable shapes. MATERIALS HORIZONS 2024; 11:1054-1064. [PMID: 38084052 DOI: 10.1039/d3mh01480k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Self-organization by the directed migration of components within a system is an important process in many applications, such as the unidirectional migration of motor proteins for transporting items to specific sites in a cell. This manuscript describes a class of functional polymeric molecules that have a set of instructions written by specific chemical moieties. These instructions allow the functional polymeric molecules to be used for autonomous synthesis of particles: particles with both functional core-shell structure and customizable shapes are fabricated for the first time. The functional polymeric molecules direct the large-scale migration of the liquid molecules to specific sites for forming the required customized structure of the particle, thus overcoming previous challenges of fabricating this class of particles. This first synthesis of this class of particles enables the development of novel applications: the concept of shape specificity for targeting sites. Both the basic structural properties (core-shell structure and customizable shape) are used in the specific applications of targeted drug delivery and imaging. The secure physical fit due to the complementary shapes enables the particles to remain locked in position for the targeting. Polymeric molecules are first shown to be highly capable of being encoded with instructions for autonomous synthesis of structured materials.
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Affiliation(s)
- Linfeng Chen
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore.
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
| | - Han Rou Low
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore.
| | - Yan Jiang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore.
| | - Wan Yu Zhang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore.
| | - Chi Kit Ao
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore.
| | - Yan Jie Neriah Tan
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore.
| | - Kang Hui Lim
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore.
| | - Siowling Soh
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore.
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11
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Liu Y, van den Ent F, Löwe J. Filament structure and subcellular organization of the bacterial intermediate filament-like protein crescentin. Proc Natl Acad Sci U S A 2024; 121:e2309984121. [PMID: 38324567 PMCID: PMC10873595 DOI: 10.1073/pnas.2309984121] [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: 06/16/2023] [Accepted: 12/28/2023] [Indexed: 02/09/2024] Open
Abstract
The protein crescentin is required for the crescent shape of the freshwater bacterium Caulobacter crescentus (vibrioides). Crescentin forms a filamentous structure on the inner, concave side of the curved cells. It shares features with eukaryotic intermediate filament (IF) proteins, including the formation of static filaments based on long and parallel coiled coils, the protein's length, structural roles in cell and organelle shape determination and the presence of a coiled coil discontinuity called the "stutter." Here, we have used electron cryomicroscopy (cryo-EM) to determine the structure of the full-length protein and its filament, exploiting a crescentin-specific nanobody. The filament is formed by two strands, related by twofold symmetry, that each consist of two dimers, resulting in an octameric assembly. Crescentin subunits form longitudinal contacts head-to-head and tail-to-tail, making the entire filament non-polar. Using in vivo site-directed cysteine cross-linking, we demonstrated that contacts observed in the in vitro filament structure exist in cells. Electron cryotomography (cryo-ET) of cells expressing crescentin showed filaments on the concave side of the curved cells, close to the inner membrane, where they form a band. When comparing with current models of IF proteins and their filaments, which are also built from parallel coiled coil dimers and lack overall polarity, it emerges that IF proteins form head-to-tail longitudinal contacts in contrast to crescentin and hence several inter-dimer contacts in IFs have no equivalents in crescentin filaments. Our work supports the idea that intermediate filament-like proteins achieve their shared polymerization and mechanical properties through a variety of filament architectures.
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Affiliation(s)
- Yue Liu
- Medical Research Council Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, CambridgeCB2 0QH, United Kingdom
| | - Fusinita van den Ent
- Medical Research Council Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, CambridgeCB2 0QH, United Kingdom
| | - Jan Löwe
- Medical Research Council Laboratory of Molecular Biology, Structural Studies Division, Cambridge Biomedical Campus, CambridgeCB2 0QH, United Kingdom
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Cockx BJR, Foster T, Clegg RJ, Alden K, Arya S, Stekel DJ, Smets BF, Kreft JU. Is it selfish to be filamentous in biofilms? Individual-based modeling links microbial growth strategies with morphology using the new and modular iDynoMiCS 2.0. PLoS Comput Biol 2024; 20:e1011303. [PMID: 38422165 PMCID: PMC10947719 DOI: 10.1371/journal.pcbi.1011303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 03/18/2024] [Accepted: 02/01/2024] [Indexed: 03/02/2024] Open
Abstract
Microbial communities are found in all habitable environments and often occur in assemblages with self-organized spatial structures developing over time. This complexity can only be understood, predicted, and managed by combining experiments with mathematical modeling. Individual-based models are particularly suited if individual heterogeneity, local interactions, and adaptive behavior are of interest. Here we present the completely overhauled software platform, the individual-based Dynamics of Microbial Communities Simulator, iDynoMiCS 2.0, which enables researchers to specify a range of different models without having to program. Key new features and improvements are: (1) Substantially enhanced ease of use (graphical user interface, editor for model specification, unit conversions, data analysis and visualization and more). (2) Increased performance and scalability enabling simulations of up to 10 million agents in 3D biofilms. (3) Kinetics can be specified with any arithmetic function. (4) Agent properties can be assembled from orthogonal modules for pick and mix flexibility. (5) Force-based mechanical interaction framework enabling attractive forces and non-spherical agent morphologies as an alternative to the shoving algorithm. The new iDynoMiCS 2.0 has undergone intensive testing, from unit tests to a suite of increasingly complex numerical tests and the standard Benchmark 3 based on nitrifying biofilms. A second test case was based on the "biofilms promote altruism" study previously implemented in BacSim because competition outcomes are highly sensitive to the developing spatial structures due to positive feedback between cooperative individuals. We extended this case study by adding morphology to find that (i) filamentous bacteria outcompete spherical bacteria regardless of growth strategy and (ii) non-cooperating filaments outcompete cooperating filaments because filaments can escape the stronger competition between themselves. In conclusion, the new substantially improved iDynoMiCS 2.0 joins a growing number of platforms for individual-based modeling of microbial communities with specific advantages and disadvantages that we discuss, giving users a wider choice.
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Affiliation(s)
- Bastiaan J. R. Cockx
- Department of Environmental and Resource Engineering, Technical University of Demark, DTU Lyngby campus, Kgs. Lyngby, Denmark
| | - Tim Foster
- Centre for Computational Biology & Institute of Microbiology and Infection & School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Robert J. Clegg
- Centre for Computational Biology & Institute of Microbiology and Infection & School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Kieran Alden
- Centre for Computational Biology & Institute of Microbiology and Infection & School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Sankalp Arya
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Dov J. Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Barth F. Smets
- Department of Environmental and Resource Engineering, Technical University of Demark, DTU Lyngby campus, Kgs. Lyngby, Denmark
| | - Jan-Ulrich Kreft
- Centre for Computational Biology & Institute of Microbiology and Infection & School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
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Söllinger A, Ahlers LS, Dahl MB, Sigurðsson P, Le Noir de Carlan C, Bhattarai B, Gall C, Martin VS, Rottensteiner C, Motleleng LL, Breines EM, Verbruggen E, Ostonen I, Sigurdsson BD, Richter A, Tveit AT. Microorganisms in subarctic soils are depleted of ribosomes under short-, medium-, and long-term warming. THE ISME JOURNAL 2024; 18:wrae081. [PMID: 38722823 PMCID: PMC11126301 DOI: 10.1093/ismejo/wrae081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/26/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024]
Abstract
Physiological responses of soil microorganisms to global warming are important for soil ecosystem function and the terrestrial carbon cycle. Here, we investigate the effects of weeks, years, and decades of soil warming across seasons and time on the microbial protein biosynthesis machineries (i.e. ribosomes), the most abundant cellular macromolecular complexes, using RNA:DNA and RNA:MBC (microbial biomass carbon) ratios as proxies for cellular ribosome contents. We compared warmed soils and non-warmed controls of 15 replicated subarctic grassland and forest soil temperature gradients subject to natural geothermal warming. RNA:DNA ratios tended to be lower in the warmed soils during summer and autumn, independent of warming duration (6 weeks, 8-14 years, and > 50 years), warming intensity (+3°C, +6°C, and +9°C), and ecosystem type. With increasing temperatures, RNA:MBC ratios were also decreasing. Additionally, seasonal RNA:DNA ratios of the consecutively sampled forest showed the same temperature-driven pattern. This suggests that subarctic soil microorganisms are depleted of ribosomes under warm conditions and the lack of consistent relationships with other physicochemical parameters besides temperature further suggests temperature as key driver. Furthermore, in incubation experiments, we measured significantly higher CO2 emission rates per unit of RNA from short- and long-term warmed soils compared to non-warmed controls. In conclusion, ribosome reduction may represent a widespread microbial physiological response to warming that offers a selective advantage at higher temperatures, as energy and matter can be reallocated from ribosome synthesis to other processes including substrate uptake and turnover. This way, ribosome reduction could have a substantial effect on soil carbon dynamics.
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Affiliation(s)
- Andrea Söllinger
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
| | - Laureen S Ahlers
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
| | - Mathilde Borg Dahl
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17489 Greifswald, Germany
| | - Páll Sigurðsson
- Faculty of Environmental and Forest Sciences, Agricultural University of Iceland, Árleynir 22, 112 Reykjavík, Iceland
- Present address: Icelandic Forest Service, Austurvegi 3, 800 Selfoss, Iceland
| | - Coline Le Noir de Carlan
- Research Group Plants and Ecosystems (PLECO), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Biplabi Bhattarai
- Department of Geography, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Christoph Gall
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Victoria S Martin
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Cornelia Rottensteiner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Liabo L Motleleng
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
| | - Eva Marie Breines
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
| | - Erik Verbruggen
- Research Group Plants and Ecosystems (PLECO), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Ivika Ostonen
- Department of Geography, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Bjarni D Sigurdsson
- Faculty of Environmental and Forest Sciences, Agricultural University of Iceland, Árleynir 22, 112 Reykjavík, Iceland
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Alexander T Tveit
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
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Vu MP, Le Hanh Tran N, Lam TQ, Quynh Tran AT, Anh Le TP, Nguyen KT. Investigating the effects of ultrafine bubbles on bacterial growth. RSC Adv 2024; 14:2159-2169. [PMID: 38205233 PMCID: PMC10777100 DOI: 10.1039/d3ra07454d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Several previous studies have considered ultrafine bubbles as a potential research target because their properties can be applied in many different research areas. In particular, the interaction between UFBs and microorganisms has always been one of the aspects that receives much attention due to the high difficulty in controlling a living system. The properties of UFBs, as mobile air-water interfaces, are greatly determined by their gas cores which play a critical role in regulating microbial growth. This study aims to investigate the effects of ultrafine bubbles on bacterial growth. Two well-studied organisms were chosen as models - Escherichia coli and Staphylococcus aureus. Their growing behavior was examined based on the growth rate, phenotype and biomass. Three types of Luria-Bertani cultures were tested, including a standard culture containing distilled water, an air ultrafine bubble culture, and a hydrogen ultrafine bubble culture. The UFBs were generated via ultrasonic cavitation and stabilized by 50 μM SDS, which was proven to have negligible effects on bacterial growth. By comparing among the three cultivation conditions, the bacterial growth rates were observed to be the highest in exposure to HUFBs. The results also signified that UFBs had an enhancement on cell proliferation. On the other hand, while proposing an increase in cell density, bacteria cultured in HUFB media have their sizes decreased uniformly and significantly (p-value < 0.05). This study confirmed that bacterial growth was promoted by UFBs; and better effects recorded were due to the HUFB present in the culture media. However, the average morphological size of bacteria was in negative correlation with their population size.
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Affiliation(s)
- Mai Phuong Vu
- School of Biotechnology, International University, Vietnam National University Ho Chi Minh City 700000 Vietnam +84 28 3724 4271 +84 28 3724 4270
| | - Nguyen Le Hanh Tran
- School of Biotechnology, International University, Vietnam National University Ho Chi Minh City 700000 Vietnam +84 28 3724 4271 +84 28 3724 4270
| | - Thien Quang Lam
- School of Biotechnology, International University, Vietnam National University Ho Chi Minh City 700000 Vietnam +84 28 3724 4271 +84 28 3724 4270
| | - Anh Thi Quynh Tran
- School of Biotechnology, International University, Vietnam National University Ho Chi Minh City 700000 Vietnam +84 28 3724 4271 +84 28 3724 4270
| | - Thu Phan Anh Le
- School of Biotechnology, International University, Vietnam National University Ho Chi Minh City 700000 Vietnam +84 28 3724 4271 +84 28 3724 4270
| | - Khoi Tan Nguyen
- School of Biotechnology, International University, Vietnam National University Ho Chi Minh City 700000 Vietnam +84 28 3724 4271 +84 28 3724 4270
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15
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Salas-Orozco MF, Lorenzo-Leal AC, de Alba Montero I, Marín NP, Santana MAC, Bach H. Mechanism of escape from the antibacterial activity of metal-based nanoparticles in clinically relevant bacteria: A systematic review. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2024; 55:102715. [PMID: 37907198 DOI: 10.1016/j.nano.2023.102715] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/05/2023] [Accepted: 10/05/2023] [Indexed: 11/02/2023]
Abstract
The emergency of antibiotic-resistant bacteria in severe infections is increasing, especially in nosocomial environments. The ESKAPE group is of special importance in the groups of multi-resistant bacteria due to its high capacity to generate resistance to antibiotics and bactericides. Therefore, metal-based nanomaterials are an attractive alternative to combat them because they have been demonstrated to damage biomolecules in the bacterial cells. However, there is a concern about bacteria developing resistance to NPs and their harmful effects due to environmental accumulation. Therefore, this systematic review aims to report the clinically relevant bacteria that have developed resistance to the NPs. According to the results of this systematic review, various mechanisms to counteract the antimicrobial activity of various NP types have been proposed. These mechanisms can be grouped into the following categories: production of extracellular compounds, metal efflux pumps, ROS response, genetic changes, DNA repair, adaptative morphogenesis, and changes in the plasma membrane.
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Affiliation(s)
- Marco Felipe Salas-Orozco
- Facultad de Estomatología, Doctorado en Ciencias Odontológicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico.
| | - Ana Cecilia Lorenzo-Leal
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Nuria Patiño Marín
- Facultad de Estomatología, Laboratorio de Investigación Clinica, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Miguel Angel Casillas Santana
- Maestría en Estomatología con Opcion Terminal en Ortodoncia, Facultad de Estomatología, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Horacio Bach
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
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Sannino DR, Arroyo FA, Pepe-Ranney C, Chen W, Volland JM, Elisabeth NH, Angert ER. The exceptional form and function of the giant bacterium Ca. Epulopiscium viviparus revolves around its sodium motive force. Proc Natl Acad Sci U S A 2023; 120:e2306160120. [PMID: 38109545 PMCID: PMC10756260 DOI: 10.1073/pnas.2306160120] [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: 04/16/2023] [Accepted: 11/09/2023] [Indexed: 12/20/2023] Open
Abstract
Epulopiscium spp. are the largest known heterotrophic bacteria; a large cigar-shaped individual is a million times the volume of Escherichia coli. To better understand the metabolic potential and relationship of Epulopiscium sp. type B with its host Naso tonganus, we generated a high-quality draft genome from a population of cells taken from a single fish. We propose the name Candidatus Epulopiscium viviparus to describe populations of this best-characterized Epulopiscium species. Metabolic reconstruction reveals more than 5% of the genome codes for carbohydrate active enzymes, which likely degrade recalcitrant host-diet algal polysaccharides into substrates that may be fermented to acetate, the most abundant short-chain fatty acid in the intestinal tract. Moreover, transcriptome analyses and the concentration of sodium ions in the host intestinal tract suggest that the use of a sodium motive force (SMF) to drive ATP synthesis and flagellar rotation is integral to symbiont metabolism and cellular biology. In natural populations, genes encoding both F-type and V-type ATPases and SMF generation via oxaloacetate decarboxylation are among the most highly expressed, suggesting that ATPases synthesize ATP and balance ion concentrations across the cell membrane. High expression of these and other integral membrane proteins may allow for the growth of its extensive intracellular membrane system. Further, complementary metabolism between microbe and host is implied with the potential provision of nitrogen and B vitamins to reinforce this nutritional symbiosis. The few features shared by all bacterial behemoths include extreme polyploidy, polyphosphate synthesis, and thus far, they have all resisted cultivation in the lab.
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Affiliation(s)
| | | | - Charles Pepe-Ranney
- Soil & Crop Sciences Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY14853
| | - Wenbo Chen
- Department of Microbiology, Cornell University, Ithaca, NY14853
| | - Jean-Marie Volland
- Laboratory for Research in Complex Systems, Menlo Park, CA94025
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Nathalie H. Elisabeth
- Department of Energy Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA94720
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17
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Tyumina E, Bazhutin G, Kostrikina N, Sorokin V, Mulyukin A, Ivshina I. Phenotypic and metabolic adaptations of Rhodococcus cerastii strain IEGM 1243 to separate and combined effects of diclofenac and ibuprofen. Front Microbiol 2023; 14:1275553. [PMID: 38125575 PMCID: PMC10730942 DOI: 10.3389/fmicb.2023.1275553] [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: 08/10/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction The increasing use of non-steroidal anti-inflammatory drugs (NSAIDs) has raised concerns regarding their environmental impact. To address this, understanding the effects of NSAIDs on bacteria is crucial for bioremediation efforts in pharmaceutical-contaminated environments. The primary challenge in breaking down persistent compounds lies not in the biochemical pathways but in capacity of bacteria to surmount stressors. Methods In this study, we examined the biodegradative activity, morphological and physiological changes, and ultrastructural adaptations of Rhodococcus cerastii strain IEGM 1243 when exposed to ibuprofen, diclofenac, and their mixture. Results and Discussion Our findings revealed that R. cerastii IEGM 1243 exhibited moderate biodegradative activity towards the tested NSAIDs. Cellular respiration assay showed higher metabolic activity in the presence of NSAIDs, indicating their influence on bacterial metabolism. Furthermore, catalase activity in R. cerastii IEGM 1243 exposed to NSAIDs showed an initial decrease followed by fluctuations, with the most significant changes observed in the presence of DCF and the NSAID mixture, likely influenced by bacterial growth phases, active NSAID degradation, and the formation of multicellular aggregates, suggesting potential intercellular synergy and task distribution within the bacterial community. Morphometric analysis demonstrated alterations in size, shape, and surface roughness of cells exposed to NSAIDs, with a decrease in surface area and volume, and an increase in surface area-to-volume ratio (SA/V). Moreover, for the first time, transmission electron microscopy confirmed the presence of lipid inclusions, polyphosphates, and intracellular membrane-like structures in the ibuprofen-treated cells. Conclusion These results provide valuable insights into the adaptive responses of R. cerastii IEGM 1243 to NSAIDs, shedding light on the possible interaction between bacteria and pharmaceutical compounds in the environment.
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Affiliation(s)
- Elena Tyumina
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, Institute of Ecology and Genetics of Microorganisms, Perm, Russia
- Department of Microbiology and Immunology, Perm State University, Perm, Russia
| | - Grigory Bazhutin
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, Institute of Ecology and Genetics of Microorganisms, Perm, Russia
- Department of Microbiology and Immunology, Perm State University, Perm, Russia
| | - Nadezhda Kostrikina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir Sorokin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Mulyukin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Irina Ivshina
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, Institute of Ecology and Genetics of Microorganisms, Perm, Russia
- Department of Microbiology and Immunology, Perm State University, Perm, Russia
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18
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Aliperti L, Aptekmann AA, Farfañuk G, Couso LL, Soler-Bistué A, Sánchez IE. r/K selection of GC content in prokaryotes. Environ Microbiol 2023; 25:3255-3268. [PMID: 37813828 DOI: 10.1111/1462-2920.16511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/16/2023] [Indexed: 10/11/2023]
Abstract
The guanine/cytosine (GC) content of prokaryotic genomes is species-specific, taking values from 16% to 77%. This diversity of selection for GC content remains contentious. We analyse the correlations between GC content and a range of phenotypic and genotypic data in thousands of prokaryotes. GC content integrates well with these traits into r/K selection theory when phenotypic plasticity is considered. High GC-content prokaryotes are r-strategists with cheaper descendants thanks to a lower average amino acid metabolic cost, colonize unstable environments thanks to flagella and a bacillus form and are generalists in terms of resource opportunism and their defence mechanisms. Low GC content prokaryotes are K-strategists specialized for stable environments that maintain homeostasis via a high-cost outer cell membrane and endospore formation as a response to nutrient deprivation, and attain a higher nutrient-to-biomass yield. The lower proteome cost of high GC content prokaryotes is driven by the association between GC-rich codons and cheaper amino acids in the genetic code, while the correlation between GC content and genome size may be partly due to functional diversity driven by r/K selection. In all, molecular diversity in the GC content of prokaryotes may be a consequence of ecological r/K selection.
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Affiliation(s)
- Lucio Aliperti
- Facultad de Ciencias Exactas y Naturales. Laboratorio de Fisiología de Proteínas, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ariel A Aptekmann
- Marine and Coastal Sciences Department, Rutgers University, New Brunswick, New Jersey, USA
| | - Gonzalo Farfañuk
- Facultad de Ciencias Exactas y Naturales. Laboratorio de Fisiología de Proteínas, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Luciana L Couso
- Facultad de Agronomía, Cátedra de Genética, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alfonso Soler-Bistué
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde, CONICET, Universidad Nacional de San Martín, San Martin, Argentina
| | - Ignacio E Sánchez
- Facultad de Ciencias Exactas y Naturales. Laboratorio de Fisiología de Proteínas, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, Buenos Aires, Argentina
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El-Nour SAA, Hammad AA, Fathy R, Eid AS. Application of coliphage as biocontrol agent in combination with gamma irradiation to eliminate multi-drug-resistant E. coli in minimally processed vegetables. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:123907-123924. [PMID: 37995029 PMCID: PMC10746767 DOI: 10.1007/s11356-023-31071-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/12/2023] [Indexed: 11/24/2023]
Abstract
Biofilm formation is a rising concern in the food industry. Escherichia coli (E. coli) is one of the most important food-borne pathogens that can survive in food and food-related environments and eventually produce biofilms. This study suggested that both coliphages used were successful in preventing the creation of new biofilms as well as removing existing ones. Confocal laser scanning microscopy verified these findings. According to the findings, neither coliphage survived at 37 °C, but both remained stable at 4 °C and - 20 °C for extended periods of time. The study revealed that both coliphages demonstrated a greater degree of gamma irradiation resistance when compared to E. coli. The study's results indicate that the implementation of a dual method, which incorporates gamma irradiation (1.5 kGy) and coliphage treatment, on various kinds of vegetables that were infected with E. coli, resulted in a significant reduction in bacterial count (surpassing 99.99%) following a 24-h incubation period. Combining gamma irradiation and the coliphage approach was significantly effective at lowering polysaccharide concentrations and proteins in the biofilm matrix. The results revealed that the pairing of gamma irradiation and coliphages acted in conjunction to cause disruptions in the matrix of biofilm, thereby promoting cell removal compared with either of the individual treatments. Ca+ ions strengthen the weak virion interaction with the relevant bacterial host cell receptors during the adsorption process. In conclusion, use of coliphage in combination with gamma irradiation treatment can be applied to improve fresh produce's microbial safety and enhance its storability in supermarkets.
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Affiliation(s)
- Salwa A Abou El-Nour
- Radiation Microbiology Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt
| | - Ali A Hammad
- Radiation Microbiology Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt
| | - Reham Fathy
- Radiation Microbiology Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt.
| | - Amal S Eid
- Radiation Microbiology Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt
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20
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Mortier J, Govers SK, Cambré A, Van Eyken R, Verheul J, den Blaauwen T, Aertsen A. Protein aggregates act as a deterministic disruptor during bacterial cell size homeostasis. Cell Mol Life Sci 2023; 80:360. [PMID: 37971522 PMCID: PMC11072981 DOI: 10.1007/s00018-023-05002-4] [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: 05/02/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 11/19/2023]
Abstract
Mechanisms underlying deviant cell size fluctuations among clonal bacterial siblings are generally considered to be cryptic and stochastic in nature. However, by scrutinizing heat-stressed populations of the model bacterium Escherichia coli, we uncovered the existence of a deterministic asymmetry in cell division that is caused by the presence of intracellular protein aggregates (PAs). While these structures typically locate at the cell pole and segregate asymmetrically among daughter cells, we now show that the presence of a polar PA consistently causes a more distal off-center positioning of the FtsZ division septum. The resulting increased length of PA-inheriting siblings persists over multiple generations and could be observed in both E. coli and Bacillus subtilis populations. Closer investigation suggests that a PA can physically perturb the nucleoid structure, which subsequently leads to asymmetric septation.
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Affiliation(s)
- Julien Mortier
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Sander K Govers
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | - Alexander Cambré
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Ronald Van Eyken
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Jolanda Verheul
- Swammerdam Institute for Life Sciences, Bacterial Cell Biology and Physiology, University of Amsterdam, Amsterdam, The Netherlands
| | - Tanneke den Blaauwen
- Swammerdam Institute for Life Sciences, Bacterial Cell Biology and Physiology, University of Amsterdam, Amsterdam, The Netherlands
| | - Abram Aertsen
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium.
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Goudin A, Ferat JL, Possoz C, Barre FX, Galli E. Recovery of Vibrio cholerae polarized cellular organization after exit from a non-proliferating spheroplast state. PLoS One 2023; 18:e0293276. [PMID: 37883451 PMCID: PMC10602287 DOI: 10.1371/journal.pone.0293276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
Vibrio cholerae, the causative agent of cholera epidemics, is a rod-shaped bacterium with a highly polarized cellular organization. It can survive harmful growth conditions by entering a non-proliferating spheroplast state, which involves loss of the cell envelope and polarity. How polarized rod organization cells are formed when the spheroplasts exit the non-proliferating state remains largely uncharacterized. To address this question, we investigated how L-arabinose-induced V. cholerae spheroplasts return to growth. We found that de novo morphogenesis started with the elimination of an excess of periplasm, which was immediately followed by cell elongation and the formation of cell branches with a diameter similar to that of normal V. cholerae cells. Periplasm elimination was driven by bifunctional peptidoglycan synthases involved in cell-wall maintenance, the aPBPs. Elongation and branching relied on the MreB-associated monofunctional peptidoglycan synthase PBP2. The cell division monofunctional peptidoglycan synthase FtsI was not involved in any of these processes. However, the FtsK cell division protein specifically targeted the sites of vesicle extrusion. Genetic material was amplified by synchronous waves of DNA replication as periplasmic elimination began. The HubP polarity factor targeted the tip of the branches as they began to form. However, HubP-mediated polarization was not involved in the efficiency of the recovery process. Finally, our results suggest that the positioning of HubP and the activities of the replication terminus organizer of the two V. cholerae chromosomes, MatP, are independent of cell division. Taken together, these results confirm the interest of L-arabinose-induced V. cholerae spheroplasts to study how cell shape is generated and shed light on the de novo establishment of the intracellular organization and cell polarization in V. cholerae.
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Affiliation(s)
- Anthony Goudin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Jean-Luc Ferat
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Christophe Possoz
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - François-Xavier Barre
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Elisa Galli
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
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22
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Adamczyk Z, Sadowska M, Nattich-Rak M. Quantifying Nanoparticle Layer Topography: Theoretical Modeling and Atomic Force Microscopy Investigations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:15067-15077. [PMID: 37824293 PMCID: PMC10601541 DOI: 10.1021/acs.langmuir.3c02024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/14/2023] [Indexed: 10/14/2023]
Abstract
A comprehensive method consisting of theoretical modeling and experimental atomic force microscopy (AFM) measurements was developed for the quantitative analysis of nanoparticle layer topography. Analytical results were derived for particles of various shapes such as cylinders (rods), disks, ellipsoids, hemispheres (caps), etc. It was shown that for all particles, their root-mean-square (rms) parameter exhibited a maximum at the coverage about 0.5, whereas the skewness was a monotonically decreasing function of the coverage. This enabled a facile determination of the particle coverage in the layer, even if the shape and size were not known. The validity of the analytical results was confirmed by computer modeling and experimental data acquired by AFM measurements for polymer nanoparticle deposition on mica and silica. The topographical analysis developed in this work can be exploited for a quantitative characterization of self-assembled layers of nano- and bioparticles, e.g., carbon nanotubes, silica and noble metal particles, DNA fragments, proteins, vesicles, viruses, and bacteria at solid surfaces. The acquired results also enabled a proper calibration, in particular the determination of the measurement precision, of various electron and scanning probe microscopies, such as AFM.
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Affiliation(s)
- Zbigniew Adamczyk
- Jerzy Haber Institute of
Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Marta Sadowska
- Jerzy Haber Institute of
Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Małgorzata Nattich-Rak
- Jerzy Haber Institute of
Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
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23
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Zhang Z, Liu Y, Zhao W, Ji M. Radiation impacts gene redundancy and biofilm regulation of cryoconite microbiomes in Northern Hemisphere glaciers. MICROBIOME 2023; 11:228. [PMID: 37848997 PMCID: PMC10583317 DOI: 10.1186/s40168-023-01621-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: 04/06/2023] [Accepted: 07/14/2023] [Indexed: 10/19/2023]
Abstract
BACKGROUND Glaciers harbor diverse microorganisms adapted to extreme conditions with high radiation, fluctuating temperature, and low nutrient availability. In glacial ecosystems, cryoconite granules are hotspots of microbial metabolic activity and could influences the biogeochemical cycle on glacier surface. Climate change could influence glacier dynamics by changing regional meteorological factors (e.g., radiation, precipitation, temperature, wind, and evaporation). Moreover, meteorological factors not only influence glacier dynamics but also directly or indirectly influence cryoconite microbiomes. However, the relationship of the meteorological factors and cryoconite microbiome are poorly understood. RESULTS Here, we collected 88 metagenomes from 26 glaciers distributed in the Northern Hemisphere with corresponding public meteorological data to reveal the relationship between meteorological factors and variation of cryoconite microbiome. Our results showed significant differences in taxonomic and genomic characteristics between cryoconite generalists and specialists. Additionally, we found that the biogeography of both generalists and specialists was influenced by solar radiation. Specialists with smaller genome size and lower gene redundancy were more abundant under high radiation stress, implying that streamlined genomes are more adapted to high radiation conditions. Network analysis revealed that biofilm regulation is a ubiquitous function in response to radiation stress, and hub genes were associated with the formation and dispersion of biofilms. CONCLUSION These findings enhance our understanding of glacier cryoconite microbiome variation on a hemispheric scale and indicate the response mechanisms to radiation stress, which will support forecasts of the ecological consequences of future climate change. Video Abstract.
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Affiliation(s)
- Zhihao Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China.
| | - Weishu Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- SJTU Yazhou Bay Institute of Deepsea Sci-Tech, Yongyou Industrial Park, Sanya, 572024, China
- International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mukan Ji
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
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24
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Psotta C, Nilsson EJ, Sjöberg T, Falk M. Bacteria-Infected Artificial Urine Characterization Based on a Combined Approach Using an Electronic Tongue Complemented with 1H-NMR and Flow Cytometry. BIOSENSORS 2023; 13:916. [PMID: 37887109 PMCID: PMC10605348 DOI: 10.3390/bios13100916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/22/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023]
Abstract
The prevailing form of bacterial infection is within the urinary tract, encompassing a wide array of bacteria that harness the urinary metabolome for their growth. Through their metabolic actions, the chemical composition of the growth medium undergoes modifications as the bacteria metabolize urine compounds, leading to the subsequent release of metabolites. These changes can indirectly indicate the existence and proliferation of bacterial organisms. Here, we investigate the use of an electronic tongue, a powerful analytical instrument based on a combination of non-selective chemical sensors with a partial specificity for data gathering combined with principal component analysis, to distinguish between infected and non-infected artificial urine samples. Three prevalent bacteria found in urinary tract infections were investigated, Escherichia coli, Klebsiella pneumoniae, and Enterococcus faecalis. Furthermore, the electronic tongue analysis was supplemented with 1H NMR spectroscopy and flow cytometry. Bacteria-specific changes in compound consumption allowed for a qualitative differentiation between artificial urine medium and bacterial growth.
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Affiliation(s)
| | | | | | - Magnus Falk
- Biomedical Science, Faculty of Health and Society, and Biofilms Research Center, Malmö University, 205 06 Malmö, Sweden; (C.P.); (E.J.N.); (T.S.)
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25
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Lough W, Weibel DB, Spagnolie SE. Self-buckling and self-writhing of semi-flexible microorganisms. SOFT MATTER 2023; 19:7349-7357. [PMID: 37740382 DOI: 10.1039/d3sm00572k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
The twisting and writhing of a cell body and associated mechanical stresses is an underappreciated constraint on microbial self-propulsion. Multi-flagellated bacteria can even buckle and writhe under their own activity as they swim through a viscous fluid. New equilibrium configurations and steady-state dynamics then emerge which depend on the organism's mechanical properties and on the oriented distribution of flagella along its surface. Modeling the cell body as a semi-flexible Kirchhoff rod and coupling the mechanics to a flagellar orientation field, we derive the Euler-Poincaré equations governing the dynamics of the system, and rationalize experimental observations of buckling and writhing of elongated swarmer cells of the bacterium Proteus mirabilis. A sequence of bifurcations is identified as the body is made more compliant, due to both buckling and torsional instabilities. These studies highlight a practical requirement for the stiffness of bacteria below which self-buckling occurs and cell motility becomes ineffective.
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Affiliation(s)
- Wilson Lough
- Department of Physics, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Douglas B Weibel
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Saverio E Spagnolie
- Department of Mathematics, University of Wisconsin-Madison, 480 Lincoln Dr, Madison, WI 53706, USA
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
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26
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Dedysh SN. Describing difficult-to-culture bacteria: Taking a shortcut or investing time to discover something new? Syst Appl Microbiol 2023; 46:126439. [PMID: 37413783 DOI: 10.1016/j.syapm.2023.126439] [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: 02/27/2023] [Revised: 06/17/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
Despite the growing interest in isolating representatives of poorly studied and as-yet-uncultivated bacterial phylogenetic groups, these microorganisms remain difficult objects for taxonomic studies. The time required for describing one of these fastidious bacteria is commonly measured in several years. What is even more problematic, many routine laboratory tests, which were originally developed for fast-growing and fast-responding microorganisms, are not fully suitable for many environmentally relevant, slow-growing bacteria. Standard techniques used in chemotaxonomic analyses do not identify unique lipids produced by these bacteria. A common practice of preparing taxonomic descriptions that report a minimal set of features to name a newly isolated organism deepens a gap between microbial ecologists and taxonomists. By contrast, investing time in detailed analysis of cell biology and experimental verification of genome-encoded capabilities of newly isolated microorganisms opens a window for novel, unexpected findings, which may shape our ideas about the functional role of these microbes in the environment.
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Affiliation(s)
- Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.
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27
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Wang Y, Wang X, Wu H, Wang L, Wang H, Lu Z. Characterization of Hsp17, a Novel Small Heat Shock Protein, in Sphingomonas melonis TY under Heat Stress. Microbiol Spectr 2023; 11:e0136023. [PMID: 37436164 PMCID: PMC10434288 DOI: 10.1128/spectrum.01360-23] [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: 03/29/2023] [Accepted: 06/24/2023] [Indexed: 07/13/2023] Open
Abstract
Bacteria are constantly exposed to a variety of environmental stresses. Temperature is considered one of the most important environmental factors affecting microbial growth and survival. As ubiquitous environmental microorganisms, Sphingomonas species play essential roles in the biodegradation of organic contaminants, plant protection, and environmental remediation. Understanding the mechanism by which they respond to heat shock will help further improve cell resistance by applying synthetic biological strategies. Here, we assessed the transcriptomic and proteomic responses of Sphingomonas melonis TY to heat shock and found that stressful conditions caused significant changes in functional genes related to protein synthesis at the transcriptional level. The most notable changes observed were increases in the transcription (1,857-fold) and protein expression (11-fold) of Hsp17, which belongs to the small heat shock protein family, and the function of Hsp17 in heat stress was further investigated in this study. We found that the deletion of hsp17 reduced the capacity of the cells to tolerate high temperatures, whereas the overexpression of hsp17 significantly enhanced the ability of the cells to withstand high temperatures. Moreover, the heterologous expression of hsp17 in Escherichia coli DH5α conferred to the bacterium the ability to resist heat stress. Interestingly, its cells were elongated and formed connected cells following the increase in temperature, while hsp17 overexpression restored their normal morphology under high temperature. In general, these results indicate that the novel small heat shock protein Hsp17 greatly contributes to maintaining cell viability and morphology under stress conditions. IMPORTANCE Temperature is generally considered the most important factor affecting metabolic functions and the survival of microbes. As molecular chaperones, small heat shock proteins can prevent damaged protein aggregation during abiotic stress, especially heat stress. Sphingomonas species are widely distributed in nature, and they can frequently be found in various extreme environments. However, the role of small heat shock proteins in Sphingomonas under high-temperature stress has not been elucidated. This study greatly enhances our understanding of a novel identified protein, Hsp17, in S. melonis TY in terms of its ability to resist heat stress and maintain cell morphology under high temperature, leading to a broader understanding of how microbes adapt to environmental extremes. Furthermore, our study will provide potential heat resistance elements for further enhancing cellular resistance as well as the synthetic biological applications of Sphingomonas.
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Affiliation(s)
- Yihan Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Xiaoyu Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Hao Wu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Lvjing Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Haixia Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
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28
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Hioki T, Kataoka K, Mutoh Y. Ruminococcus gnavus bacteraemia showing morphological diversity on Gram staining: a case report and literature review. Access Microbiol 2023; 5:acmi000442. [PMID: 37424554 PMCID: PMC10323785 DOI: 10.1099/acmi.0.000442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/12/2022] [Indexed: 07/11/2023] Open
Abstract
Ruminococcus gnavus , a Gram-positive anaerobic coccus, is a common constituent of the human gut microbiota but rarely causes any disease in humans. Herein, we report a case of R. gnavus bacteraemia in an immunocompromised 73-year-old man with sigmoid colon perforation. R. gnavus is usually reported as Gram-positive diplococci or short chains on Gram staining; however, in our patient, a blood isolate showed Gram-positive cocci in long chains, and organisms from an anaerobic subculture showed morphological diversity. This case provides insight into the morphological diversity of R. gnavus , which might help with the recognition of these bacteria in the preliminary identification stage on Gram staining.
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Affiliation(s)
- Tatsuya Hioki
- Department of Clinical Laboratory, Tosei General Hospital, 160 Nishioiwake-cho, Seto, Aichi, 489-8642, Japan
| | - Kensuke Kataoka
- Department of Respiratory Medicine and Allergy, Tosei General Hospital, 160 Nishioiwake-cho, Seto, Aichi, 489-8642, Japan
| | - Yoshikazu Mutoh
- Department of Infectious Diseases, Tosei General Hospital, 160 Nishioiwake-cho, Seto, Aichi, 489-8642, Japan
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29
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Rollins J, Worthington T, Dransfield A, Whitney J, Stanford J, Hooke E, Hobson J, Wengler J, Hope S, Mizrachi D. Expression of Cell-Adhesion Molecules in E. coli: A High Throughput Screening to Identify Paracellular Modulators. Int J Mol Sci 2023; 24:9784. [PMID: 37372932 DOI: 10.3390/ijms24129784] [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: 05/17/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Cell-adhesion molecules (CAMs) are responsible for cell-cell, cell-extracellular matrix, and cell-pathogen interactions. Claudins (CLDNs), occludin (OCLN), and junctional adhesion molecules (JAMs) are CAMs' components of the tight junction (TJ), the single protein structure tasked with safeguarding the paracellular space. The TJ is responsible for controlling paracellular permeability according to size and charge. Currently, there are no therapeutic solutions to modulate the TJ. Here, we describe the expression of CLDN proteins in the outer membrane of E. coli and report its consequences. When the expression is induced, the unicellular behavior of E. coli is replaced with multicellular aggregations that can be quantified using Flow Cytometry (FC). Our method, called iCLASP (inspection of cell-adhesion molecules aggregation through FC protocols), allows high-throughput screening (HTS) of small-molecules for interactions with CAMs. Here, we focused on using iCLASP to identify paracellular modulators for CLDN2. Furthermore, we validated those compounds in the mammalian cell line A549 as a proof-of-concept for the iCLASP method.
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Affiliation(s)
- Jay Rollins
- Department of Cell Biology and Physiology, College of Life Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Tyler Worthington
- Department of Cell Biology and Physiology, College of Life Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Allison Dransfield
- Department of Cell Biology and Physiology, College of Life Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Jordan Whitney
- Department of Cell Biology and Physiology, College of Life Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Jordan Stanford
- Department of Cell Biology and Physiology, College of Life Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Emily Hooke
- Department of Cell Biology and Physiology, College of Life Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Joseph Hobson
- Department of Cell Biology and Physiology, College of Life Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Jacob Wengler
- Department of Cell Biology and Physiology, College of Life Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Sandra Hope
- Department of Microbiology and Molecular Biology, College of Life Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Dario Mizrachi
- Department of Cell Biology and Physiology, College of Life Sciences, Brigham Young University, Provo, UT 84602, USA
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30
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Ale Enriquez F, Ahring BK. Strategies to overcome mass transfer limitations of hydrogen during anaerobic gaseous fermentations: A comprehensive review. BIORESOURCE TECHNOLOGY 2023; 377:128948. [PMID: 36963702 DOI: 10.1016/j.biortech.2023.128948] [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: 02/06/2023] [Revised: 03/10/2023] [Accepted: 03/20/2023] [Indexed: 06/18/2023]
Abstract
Fermentation of gaseous substrates such as carbon dioxide (CO2) has emerged as a sustainable approach for transforming greenhouse gas emissions into renewable fuels and biochemicals. CO2 fermentations are catalyzed by hydrogenotrophic methanogens and homoacetogens, these anaerobic microorganisms selectively reduce CO2 using hydrogen (H2) as electron donor. However, H2 possesses low solubility in liquid media leading to slow mass transport, limiting the reaction rates of CO2 reduction. Solving the problems of mass transport of H2 could boost the advance of technologies for valorizing industrial CO2-rich streams, like biogas or syngas. The application could further be extended to combustion flue gases or even atmospheric CO2. In this work, an overview of strategies for overcoming H2 mass transport limitations during methanogenic and acetogenic fermentation of H2 and CO2 is presented. The potential for using these strategies in future full-scale facilities and the knowledge gaps for these applications are discussed in detail.
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Affiliation(s)
- Fuad Ale Enriquez
- Bioproducts, Sciences, and Engineering Laboratory, Washington State University, Tri-Cities, Richland, WA 99354, USA; The Gene and Linda Voiland School of Chemical and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - Birgitte K Ahring
- Bioproducts, Sciences, and Engineering Laboratory, Washington State University, Tri-Cities, Richland, WA 99354, USA; The Gene and Linda Voiland School of Chemical and Bioengineering, Washington State University, Pullman, WA 99164, USA; Biological Systems Engineering Department, L.J. Smith Hall, Washington State University, Pullman, WA 99164, USA.
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31
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Richter P, Melzer B, Müller FD. Interacting bactofilins impact cell shape of the MreB-less multicellular Rhodomicrobium vannielii. PLoS Genet 2023; 19:e1010788. [PMID: 37256900 DOI: 10.1371/journal.pgen.1010788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 05/16/2023] [Indexed: 06/02/2023] Open
Abstract
Most non-spherical bacteria rely on the actin-like MreB cytoskeleton to control synthesis of a cell-shaping and primarily rod-like cell wall. Diverging from simple rod shape generally requires accessory cytoskeletal elements, which locally interfere with the MreB-guided cell wall synthesis. Conserved and widespread representatives of this accessory cytoskeleton are bactofilins that polymerize into static, non-polar bundles of filaments. Intriguingly, many species of the Actinobacteria and Rhizobiales manage to grow rod-like without MreB by tip extension, yet some of them still possess bactofilin genes, whose function in cell morphogenesis is unknown. An intricate representative of these tip-growing bacteria is Rhodomicrobium vannielii; a member of the hitherto genetically not tractable and poorly studied Hyphomicrobiaceae within the MreB-less Rhizobiales order. R. vannielii displays complex asymmetric cell shapes and differentiation patterns including filamentous hyphae to produce offspring and to build dendritic multicellular arrays. Here, we introduce techniques to genetically access R. vannielii, and we elucidate the role of bactofilins in its sophisticated morphogenesis. By targeted mutagenesis and fluorescence microscopy, protein interaction studies and peptidoglycan incorporation analysis we show that the R. vannielii bactofilins are associated with the hyphal growth zones and that one of them is essential to form proper hyphae. Another paralog is suggested to represent a novel hybrid and co-polymerizing bactofilin. Notably, we present R. vannielii as a powerful new model to understand prokaryotic cell development and control of multipolar cell growth in the absence of the conserved cytoskeletal element, MreB.
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Affiliation(s)
- Pia Richter
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
- Faculty of Biology, University of Marburg, Marburg, Germany
| | - Brigitte Melzer
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
- Max Rubner-Institute, Federal Research Institute of Nutrition and Food, Kulmbach, Germany
| | - Frank D Müller
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
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32
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Takuhei S, Nishimura Y, Yoshizawa S, Takami H, Hamasaki K, Fujiwara A, Nishino S, Harada N. Distribution and survival strategies of endemic and cosmopolitan diazotrophs in the Arctic Ocean. THE ISME JOURNAL 2023:10.1038/s41396-023-01424-x. [PMID: 37217593 DOI: 10.1038/s41396-023-01424-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/18/2023] [Accepted: 04/25/2023] [Indexed: 05/24/2023]
Abstract
Dinitrogen (N2) fixation is the major source of reactive nitrogen in the ocean and has been considered to occur specifically in low-latitude oligotrophic oceans. Recent studies have shown that N2 fixation also occurs in the polar regions and thus is a global process, although the physiological and ecological characteristics of polar diazotrophs are not yet known. Here, we successfully reconstructed diazotroph genomes, including that of cyanobacterium UCYN-A (Candidatus 'Atelocyanobacterium thalassa'), from metagenome data corresponding to 111 samples isolated from the Arctic Ocean. These diazotrophs were highly abundant in the Arctic Ocean (max., 1.28% of the total microbial community), suggesting that they have important roles in the Arctic ecosystem and biogeochemical cycles. Further, we show that diazotrophs within genera Arcobacter, Psychromonas, and Oceanobacter are prevalent in the <0.2 µm fraction in the Arctic Ocean, indicating that current methods cannot capture their N2 fixation. Diazotrophs in the Arctic Ocean were either Arctic-endemic or cosmopolitan species from their global distribution patterns. Arctic-endemic diazotrophs, including Arctic UCYN-A, were similar to low-latitude-endemic and cosmopolitan diazotrophs in genome-wide function, however, they had unique gene sets (e.g., diverse aromatics degradation genes), suggesting adaptations to Arctic-specific conditions. Cosmopolitan diazotrophs were generally non-cyanobacteria and commonly had the gene that encodes the cold-inducible RNA chaperone, which presumably makes their survival possible even in deep, cold waters of global ocean and polar surface waters. This study shows global distribution pattern of diazotrophs with their genomes and provides clues to answering the question of how diazotrophs can inhabit polar waters.
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Affiliation(s)
- Shiozaki Takuhei
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan.
| | - Yosuke Nishimura
- Research Centre for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
| | - Hideto Takami
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
- Center for Mathematical Science and Advanced Technology, JAMSTEC, Yokohama, 236-0001, Japan
| | - Koji Hamasaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 277-8564, Kashiwa, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 113-8657, Bunkyo-ku, Japan
| | - Amane Fujiwara
- Research Institute for Global Change, JAMSTEC, Yokosuka, 237-0061, Japan
| | - Shigeto Nishino
- Research Institute for Global Change, JAMSTEC, Yokosuka, 237-0061, Japan
| | - Naomi Harada
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
- Research Institute for Global Change, JAMSTEC, Yokosuka, 237-0061, Japan
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33
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Pacholak A, Juzwa W, Zgoła-Grześkowiak A, Kaczorek E. Multi-faceted analysis of bacterial transformation of nitrofurantoin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 874:162422. [PMID: 36863585 DOI: 10.1016/j.scitotenv.2023.162422] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/15/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
Excessive presence of antibiotics and their residues can be dangerous to the natural environment. To reduce this negative effect, efficient strategies to remove them from the ecosystem are required. This study aimed to explore the potential of bacterial strains to degrade nitrofurantoin (NFT). Single strains isolated from contaminated areas, namely Stenotrophomonas acidaminiphila N0B, Pseudomonas indoloxydans WB, and Serratia marcescens ODW152 were employed in this study. Degradation efficiency and dynamic changes within the cells during NFT biodegradation were investigated. For this purpose, atomic force microscopy, flow cytometry, zeta potential, and particle size distribution measurements were applied. Serratia marcescens ODW152 showed the highest performance in removal of NFT (96 % in 28 days). The AFM images revealed modifications of cell shape and surface structure induced by NFT. Zeta potential showed significant variations during biodegradation. Cultures exposed to NFT had a broader size distribution than the control cultures due to increased cells agglomeration or aggregation. 1-Aminohydantoin and semicarbazide were detected as nitrofurantoin biotransformation products. They showed increased cytotoxicity toward bacteria as determined by spectroscopy and flow cytometry. Results of this study suggest that nitrofurantoin biodegradation leads to formation of stable transformation products that significantly affect the physiology and structure of bacterial cells.
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Affiliation(s)
- Amanda Pacholak
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Poznan, Poland.
| | - Wojciech Juzwa
- Department of Biotechnology and Food Microbiology, Faculty of Food Science, Poznan University of Life Sciences, Poznan, Poland
| | | | - Ewa Kaczorek
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Poznan, Poland
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34
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Gu F, Jiang W, Kang F, Su T, Yang X, Qi Q, Liang Q. A synthetic population-level oscillator in non-microfluidic environments. Commun Biol 2023; 6:515. [PMID: 37179427 PMCID: PMC10183009 DOI: 10.1038/s42003-023-04904-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Synthetic oscillators have become a research hotspot because of their complexity and importance. The construction and stable operation of oscillators in large-scale environments are important and challenging. Here, we introduce a synthetic population-level oscillator in Escherichia coli that operates stably during continuous culture in non-microfluidic environments without the addition of inducers or frequent dilution. Specifically, quorum-sensing components and protease regulating elements are employed, which form delayed negative feedback to trigger oscillation and accomplish the reset of signals through transcriptional and post-translational regulation. We test the circuit in devices with 1 mL, 50 mL, 400 mL of medium, and demonstrate that the circuit could maintain stable population-level oscillations. Finally, we explore potential applications of the circuit in regulating cellular morphology and metabolism. Our work contributes to the design and testing of synthetic biological clocks that function in large populations.
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Affiliation(s)
- Fei Gu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72, Binhai Road, 266237, Qingdao, China
| | - Wei Jiang
- Research Center of Basic Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Fangbing Kang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72, Binhai Road, 266237, Qingdao, China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, No. 72, Binhai Road, 266237, Qingdao, China
| | - Xiaoya Yang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72, Binhai Road, 266237, Qingdao, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, No. 72, Binhai Road, 266237, Qingdao, China.
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72, Binhai Road, 266237, Qingdao, China.
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35
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Noba K, Yoshimoto S, Tanaka Y, Yokoyama T, Matsuura T, Hori K. Simple Method for the Creation of a Bacteria-Sized Unilamellar Liposome with Different Proteins Localized to the Respective Sides of the Membrane. ACS Synth Biol 2023; 12:1437-1446. [PMID: 37155350 DOI: 10.1021/acssynbio.2c00564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Artificial cells are membrane vesicles mimicking cellular functions. To date, giant unilamellar vesicles made from a single lipid membrane with a diameter of 10 μm or more have been used to create artificial cells. However, the creation of artificial cells that mimic the membrane structure and size of bacteria has been limited due to technical restrictions of conventional liposome preparation methods. Here, we created bacteria-sized large unilamellar vesicles (LUVs) with proteins localized asymmetrically to the lipid bilayer. Liposomes containing benzylguanine-modified phospholipids were prepared by combining the conventional water-in-oil emulsion method and the extruder method, and green fluorescent protein fused with SNAP-tag was localized to the inner leaflet of the lipid bilayer. Biotinylated lipid molecules were then inserted externally, and the outer leaflet was modified with streptavidin. The resulting liposomes had a size distribution in the range of 500-2000 nm with a peak at 841 nm (the coefficient of variation was 10.3%), which was similar to that of spherical bacterial cells. Fluorescence microscopy, quantitative evaluation using flow cytometry, and western blotting proved the intended localization of different proteins on the lipid membrane. Cryogenic electron microscopy and quantitative evaluation by α-hemolysin insertion revealed that most of the created liposomes were unilamellar. Our simple method for the preparation of bacteria-sized LUVs with asymmetrically localized proteins will contribute to the creation of artificial bacterial cells for investigating functions and the significance of their surface structure and size.
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Affiliation(s)
- Kosaku Noba
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Shogo Yoshimoto
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Yoshikazu Tanaka
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-Ku, Sendai 980-8577, Japan
| | - Takeshi Yokoyama
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-Ku, Sendai 980-8577, Japan
| | - Tomoaki Matsuura
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1-i7E-307, Meguro-Ku, Tokyo 152-8550, Japan
| | - Katsutoshi Hori
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
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36
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Kratz JC, Banerjee S. Dynamic proteome trade-offs regulate bacterial cell size and growth in fluctuating nutrient environments. Commun Biol 2023; 6:486. [PMID: 37147517 PMCID: PMC10163005 DOI: 10.1038/s42003-023-04865-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/24/2023] [Indexed: 05/07/2023] Open
Abstract
Bacteria dynamically regulate cell size and growth to thrive in changing environments. While previous studies have characterized bacterial growth physiology at steady-state, a quantitative understanding of bacterial physiology in time-varying environments is lacking. Here we develop a quantitative theory connecting bacterial growth and division rates to proteome allocation in time-varying nutrient environments. In such environments, cell size and growth are regulated by trade-offs between prioritization of biomass accumulation or division, resulting in decoupling of single-cell growth rate from population growth rate. Specifically, bacteria transiently prioritize biomass accumulation over production of division machinery during nutrient upshifts, while prioritizing division over growth during downshifts. When subjected to pulsatile nutrient concentration, we find that bacteria exhibit a transient memory of previous metabolic states due to the slow dynamics of proteome reallocation. This allows for faster adaptation to previously seen environments and results in division control which is dependent on the time-profile of fluctuations.
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Affiliation(s)
- Josiah C Kratz
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Shiladitya Banerjee
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
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37
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Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles. NANO LETTERS 2023; 23:4267-4273. [PMID: 37141427 DOI: 10.1021/acs.nanolett.3c00375] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Endocytosis is a key cellular process involved in the uptake of nutrients, pathogens, or the therapy of diseases. Most studies have focused on spherical objects, whereas biologically relevant shapes can be highly anisotropic. In this letter, we use an experimental model system based on Giant Unilamellar Vesicles (GUVs) and dumbbell-shaped colloidal particles to mimic and investigate the first stage of the passive endocytic process: engulfment of an anisotropic object by the membrane. Our model has specific ligand-receptor interactions realized by mobile receptors on the vesicles and immobile ligands on the particles. Through a series of experiments, theory, and molecular dynamics simulations, we quantify the wrapping process of anisotropic dumbbells by GUVs and identify distinct stages of the wrapping pathway. We find that the strong curvature variation in the neck of the dumbbell as well as membrane tension are crucial in determining both the speed of wrapping and the final states.
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Affiliation(s)
- Ali Azadbakht
- Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO Box 9504, 2300 RA Leiden, The Netherlands
| | - Billie Meadowcroft
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Thijs Varkevisser
- Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO Box 9504, 2300 RA Leiden, The Netherlands
- Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - Anđela Šarić
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Daniela J Kraft
- Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO Box 9504, 2300 RA Leiden, The Netherlands
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38
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Piano E, Biagioli F, Nicolosi G, Coleine C, Poli A, Prigione V, Zanellati A, Addesso R, Varese GC, Selbmann L, Isaia M. Tourism affects microbial assemblages in show caves. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:162106. [PMID: 36764528 DOI: 10.1016/j.scitotenv.2023.162106] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/30/2023] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
Anthropogenic disturbance on natural ecosystems is growing in frequency and magnitude affecting all ecosystems components. Understanding the response of different types of biocoenosis to human disturbance is urgently needed and it can be achieved by adopting a metacommunity framework. With the aid of advanced molecular techniques, we investigated sediment communities of Fungi, Bacteria and Archaea in four Italian show caves, aiming to disentangle the effects induced by tourism on their diversity and to highlight changes in the driving forces that shape their community composition. We modelled diversity measures against proxies of tourism pressure. With this approach we demonstrate that the cave tourism has a direct effect on the community of Bacteria and an indirect influence on Fungi and Archaea. By analysing the main driving forces influencing the community composition of the three microbial groups, we highlighted that stochastic factors override dispersal-related processes and environmental selection in show caves compared to undisturbed areas. Thanks to this approach, we provide new perspectives on the dynamics of microbial communities under human disturbance suggesting that a proper understanding of the underlying selective mechanisms requires a comprehensive and multi-taxonomic approach.
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Affiliation(s)
- Elena Piano
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy
| | - Federico Biagioli
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy
| | - Giuseppe Nicolosi
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy
| | - Anna Poli
- Mycotheca Universitatis Taurinensis, Department of Life Sciences and Systems Biology, University of Torino, Viale Mattioli 25, 10125 Torino, Italy
| | - Valeria Prigione
- Mycotheca Universitatis Taurinensis, Department of Life Sciences and Systems Biology, University of Torino, Viale Mattioli 25, 10125 Torino, Italy
| | - Andrea Zanellati
- Mycotheca Universitatis Taurinensis, Department of Life Sciences and Systems Biology, University of Torino, Viale Mattioli 25, 10125 Torino, Italy
| | - Rosangela Addesso
- Department of Chemistry and Biology "Adolfo Zambelli", University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy
| | - Giovanna Cristina Varese
- Mycotheca Universitatis Taurinensis, Department of Life Sciences and Systems Biology, University of Torino, Viale Mattioli 25, 10125 Torino, Italy
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy
| | - Marco Isaia
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy.
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Abstract
Bacteria thrive in environments rich in fluid flow, such as the gastrointestinal tract, bloodstream, aquatic systems, and the urinary tract. Despite the importance of flow, how flow affects bacterial life is underappreciated. In recent years, the combination of approaches from biology, physics, and engineering has led to a deeper understanding of how bacteria interact with flow. Here, we highlight the wide range of bacterial responses to flow, including changes in surface adhesion, motility, surface colonization, quorum sensing, virulence factor production, and gene expression. To emphasize the diversity of flow responses, we focus our review on how flow affects four ecologically distinct bacterial species: Escherichia coli, Staphylococcus aureus, Caulobacter crescentus, and Pseudomonas aeruginosa. Additionally, we present experimental approaches to precisely study bacteria in flow, discuss how only some flow responses are triggered by shear force, and provide perspective on flow-sensitive bacterial signaling.
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Affiliation(s)
- Gilberto C. Padron
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Alexander M. Shuppara
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jessica-Jae S. Palalay
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Anuradha Sharma
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Joseph E. Sanfilippo
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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40
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Maimone G, Azzaro M, Placenti F, Paranhos R, Cabral AS, Decembrini F, Zaccone R, Cosenza A, Rappazzo AC, Patti B, Basilone G, Cuttitta A, Ferreri R, Aronica S, Ferla RL. A Morphometric Approach to Understand Prokaryoplankton: A Study in the Sicily Channel (Central Mediterranean Sea). Microorganisms 2023; 11:microorganisms11041019. [PMID: 37110442 PMCID: PMC10142791 DOI: 10.3390/microorganisms11041019] [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: 03/08/2023] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
A new understanding of plankton ecology has been obtained by studying the phenotypic traits of free-living prokaryotes in the Sicily Channel (Central Mediterranean Sea), an area characterised by oligotrophic conditions. During three cruises carried out in July 2012, January 2013 and July 2013, the volume and morphology of prokaryotic cells were assessed microscopically using image analysis in relation to environmental conditions. The study found significant differences in cell morphologies among cruises. The largest cell volumes were observed in the July 2012 cruise (0.170 ± 0.156 µm3), and the smallest in the January 2013 cruise (0.060 ± 0.052 µm3). Cell volume was negatively limited by nutrients and positively by salinity. Seven cellular morphotypes were observed among which cocci, rods and coccobacilli were the most abundant. Cocci, although they prevailed numerically, always showed the smallest volumes. Elongated shapes were positively related to temperature. Relationships between cell morphologies and environmental drivers indicated a bottom-up control of the prokaryotic community. The morphology/morphometry-based approach is a useful tool for studying the prokaryotic community in microbial ecology and should be widely applied to marine microbial populations in nature.
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Affiliation(s)
- Giovanna Maimone
- Institute of Polar Sciences, CNR ISP, Spianata S. Raineri 82, 98122 Messina, Italy
| | - Maurizio Azzaro
- Institute of Polar Sciences, CNR ISP, Spianata S. Raineri 82, 98122 Messina, Italy
| | - Francesco Placenti
- Institute of Anthropic Impacts and Sustainability in the Marine Environment, CNR IAS, Via del Mare 3, 91021 Capo Granitola, Italy
| | - Rodolfo Paranhos
- Laboratory of Hydrobiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Av. Prof. Rodolpho Rocco 211, Rio de Janeiro 21941 617, Brazil
| | - Anderson Sousa Cabral
- Laboratory of Hydrobiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Av. Prof. Rodolpho Rocco 211, Rio de Janeiro 21941 617, Brazil
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho 373, Rio de Janeiro 21941 902, Brazil
| | - Franco Decembrini
- Institute of Polar Sciences, CNR ISP, Spianata S. Raineri 82, 98122 Messina, Italy
| | - Renata Zaccone
- Institute of Polar Sciences, CNR ISP, Spianata S. Raineri 82, 98122 Messina, Italy
| | - Alessandro Cosenza
- Institute of Polar Sciences, CNR ISP, Spianata S. Raineri 82, 98122 Messina, Italy
| | - Alessandro Ciro Rappazzo
- Institute of Polar Sciences, CNR ISP, Spianata S. Raineri 82, 98122 Messina, Italy
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari Unversity of Venice Campus Scientifico, Via Torino 155, 30170 Venice, Italy
| | - Bernardo Patti
- Institute of Anthropic Impacts and Sustainability in the Marine Environment, CNR IAS, Lungomare Cristoforo Colombo 4521, 90149 Palermo, Italy
| | - Gualtiero Basilone
- Institute of Anthropic Impacts and Sustainability in the Marine Environment, CNR IAS, Via del Mare 3, 91021 Capo Granitola, Italy
| | - Angela Cuttitta
- Institute for Studies on the Mediterranean, CNR ISMED, Via Filippo Parlatore 65, 90145 Palermo, Italy
| | - Rosalia Ferreri
- Institute of Anthropic Impacts and Sustainability in the Marine Environment, CNR IAS, Via del Mare 3, 91021 Capo Granitola, Italy
| | - Salvatore Aronica
- Institute of Anthropic Impacts and Sustainability in the Marine Environment, CNR IAS, Via del Mare 3, 91021 Capo Granitola, Italy
| | - Rosabruna La Ferla
- Institute of Polar Sciences, CNR ISP, Spianata S. Raineri 82, 98122 Messina, Italy
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41
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Dudek NK, Galaz-Montoya JG, Shi H, Mayer M, Danita C, Celis AI, Viehboeck T, Wu GH, Behr B, Bulgheresi S, Huang KC, Chiu W, Relman DA. Previously uncharacterized rectangular bacterial structures in the dolphin mouth. Nat Commun 2023; 14:2098. [PMID: 37055390 PMCID: PMC10102025 DOI: 10.1038/s41467-023-37638-y] [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: 11/01/2021] [Accepted: 03/23/2023] [Indexed: 04/15/2023] Open
Abstract
Much remains to be explored regarding the diversity of uncultured, host-associated microbes. Here, we describe rectangular bacterial structures (RBSs) in the mouths of bottlenose dolphins. DNA staining revealed multiple paired bands within RBSs, suggesting the presence of cells dividing along the longitudinal axis. Cryogenic transmission electron microscopy and tomography showed parallel membrane-bound segments that are likely cells, encapsulated by an S-layer-like periodic surface covering. RBSs displayed unusual pilus-like appendages with bundles of threads splayed at the tips. We present multiple lines of evidence, including genomic DNA sequencing of micromanipulated RBSs, 16S rRNA gene sequencing, and fluorescence in situ hybridization, suggesting that RBSs are bacterial and distinct from the genera Simonsiella and Conchiformibius (family Neisseriaceae), with which they share similar morphology and division patterning. Our findings highlight the diversity of novel microbial forms and lifestyles that await characterization using tools complementary to genomics such as microscopy.
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Affiliation(s)
- Natasha K Dudek
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
- Quantori, Cambridge, MA, 02142, USA
| | | | - Handuo Shi
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Megan Mayer
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Cristina Danita
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Arianna I Celis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Tobias Viehboeck
- Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, University of Vienna, Vienna, Austria
- Division of Microbial Ecology, Center for Microbiology and Environmental Systems Science, and Vienna Doctoral School of Ecology and Evolution, University of Vienna, Vienna, Austria
| | - Gong-Her Wu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Barry Behr
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Silvia Bulgheresi
- Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, University of Vienna, Vienna, Austria
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - David A Relman
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
- Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, 94304, USA.
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42
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Zeng X, Huang M, Sun QX, Peng YJ, Xu X, Tang YB, Zhang JY, Yang Y, Zhang CC. A c-di-GMP binding effector controls cell size in a cyanobacterium. Proc Natl Acad Sci U S A 2023; 120:e2221874120. [PMID: 36947515 PMCID: PMC10068817 DOI: 10.1073/pnas.2221874120] [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: 12/27/2022] [Accepted: 02/22/2023] [Indexed: 03/23/2023] Open
Abstract
Cyclic-di-GMP (c-di-GMP) is a ubiquitous bacterial signaling molecule. It is also a critical player in the regulation of cell size and cell behaviors such as cell aggregation and phototaxis in cyanobacteria, which constitute an important group of prokaryotes for their roles in the ecology and evolution of the Earth. However, c-di-GMP receptors have never been revealed in cyanobacteria. Here, we report the identification of a c-di-GMP receptor, CdgR, from the filamentous cyanobacterium Anabaena PCC 7120. Crystal structural analysis and genetic studies demonstrate that CdgR binds c-di-GMP at the dimer interface and this binding is required for the control of cell size in a c-di-GMP-dependent manner. Different functions of CdgR, in ligand binding and signal transmission, could be separated genetically, allowing us to dissect its molecular signaling functions. The presence of the apo-form of CdgR triggers cell size reduction, consistent with the similar effects observed with a decrease of c-di-GMP levels in cells. Furthermore, we found that CdgR exerts its function by interacting with a global transcription factor DevH, and this interaction was inhibited by c-di-GMP. The lethal effect triggered by conditional depletion of DevH or by the production of several point-mutant proteins of CdgR in cells indicates that this signaling pathway plays critical functions in Anabaena. Our studies revealed a mechanism of c-di-GMP signaling in the control of cell size, an important and complex trait for bacteria. CdgR is highly conserved in cyanobacteria, which will greatly expand our understanding of the roles of c-di-GMP signaling in these organisms.
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Affiliation(s)
- Xiaoli Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
| | - Min Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Qing-Xue Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Ye-Jun Peng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing100049, People’s Republic of China
| | - Xiaomei Xu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
| | - Yun-Bin Tang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
| | - Ju-Yuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
| | - Yiling Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
| | - Cheng-Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei430072, People’s Republic of China
- Institut AMU-WUT, Aix-Marseille Université and Wuhan University of Technology, Wuhan, Hubei430070, People’s Republic of China
- Innovation Academy for Seed Design Chinese Academy of Sciences, Beijing100049, People’s Republic of China
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L Pastrana C, Qiu L, Armon S, Gerland U, Amir A. Pressure-induced shape-shifting of helical bacteria. SOFT MATTER 2023; 19:2224-2230. [PMID: 36884021 DOI: 10.1039/d2sm01044e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Many bacterial species are helical in shape, including the widespread pathogen H. pylori. Motivated by recent experiments on H. pylori showing that cell wall synthesis is not uniform [J. A. Taylor, et al., eLife, 2020, 9, e52482], we investigate the possible formation of helical cell shape induced by elastic heterogeneity. We show, experimentally and theoretically, that helical morphogenesis can be produced by pressurizing an elastic cylindrical vessel with helical reinforced lines. The properties of the pressurized helix are highly dependent on the initial helical angle of the reinforced region. We find that steep angles result in crooked helices with, surprisingly, a reduced end-to-end distance upon pressurization. This work helps explain the possible mechanisms for the generation of helical cell morphologies and may inspire the design of novel pressure-controlled helical actuators.
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Affiliation(s)
- César L Pastrana
- Physics of Complex Biosystems, Technical University of Munich, 85748 Garching, Germany.
| | - Luyi Qiu
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA.
| | - Shahaf Armon
- Department of Physics of Complex Systems, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ulrich Gerland
- Physics of Complex Biosystems, Technical University of Munich, 85748 Garching, Germany.
| | - Ariel Amir
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA.
- Department of Physics of Complex Systems, Weizmann Institute of Science, 7610001 Rehovot, Israel
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44
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Caldwell M, Hughes M, Wei F, Ngo C, Pascua R, Pugazhendhi AS, Coathup MJ. Promising applications of D-amino acids in periprosthetic joint infection. Bone Res 2023; 11:14. [PMID: 36894568 PMCID: PMC9998894 DOI: 10.1038/s41413-023-00254-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/02/2023] [Accepted: 02/10/2023] [Indexed: 03/11/2023] Open
Abstract
Due to the rise in our aging population, a disproportionate demand for total joint arthroplasty (TJA) in the elderly is forecast. Periprosthetic joint infection (PJI) represents one of the most challenging complications that can occur following TJA, and as the number of primary and revision TJAs continues to rise, an increasing PJI burden is projected. Despite advances in operating room sterility, antiseptic protocols, and surgical techniques, approaches to prevent and treat PJI remain difficult, primarily due to the formation of microbial biofilms. This difficulty motivates researchers to continue searching for an effective antimicrobial strategy. The dextrorotatory-isoforms of amino acids (D-AAs) are essential components of peptidoglycan within the bacterial cell wall, providing strength and structural integrity in a diverse range of species. Among many tasks, D-AAs regulate cell morphology, spore germination, and bacterial survival, evasion, subversion, and adhesion in the host immune system. When administered exogenously, accumulating data have demonstrated that D-AAs play a pivotal role against bacterial adhesion to abiotic surfaces and subsequent biofilm formation; furthermore, D-AAs have substantial efficacy in promoting biofilm disassembly. This presents D-AAs as promising and novel targets for future therapeutic approaches. Despite their emerging antibacterial efficacy, their role in disrupting PJI biofilm formation, the disassembly of established TJA biofilm, and the host bone tissue response remains largely unexplored. This review aims to examine the role of D-AAs in the context of TJAs. Data to date suggest that D-AA bioengineering may serve as a promising future strategy in the prevention and treatment of PJI.
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Affiliation(s)
- Matthew Caldwell
- Biionix Cluster & College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA
| | - Megan Hughes
- School of Biosciences, Cardiff University, CF10 3AT, Wales, UK
| | - Fei Wei
- Biionix Cluster & College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA
| | - Christopher Ngo
- Biionix Cluster & College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA
| | - Raven Pascua
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA
| | - Abinaya Sindu Pugazhendhi
- Biionix Cluster & College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA
| | - Melanie J Coathup
- Biionix Cluster & College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Orlando, FL, 32827, USA.
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Control of Cell Size by c-di-GMP Requires a Two-Component Signaling System in the Cyanobacterium Anabaena sp. Strain PCC 7120. Microbiol Spectr 2023; 11:e0422822. [PMID: 36625639 PMCID: PMC9927289 DOI: 10.1128/spectrum.04228-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Each bacterial species possesses a specific cell size and morphology, which constitute important and recognizable physical traits. How bacteria maintain their particular cell size and morphology remains an essential question in microbiology. Cyanobacteria are oxygen-evolving photosynthetic prokaryotes. Although monophyletic, these organisms are highly diverse in their cell morphology and cell size. How these physical traits of cyanobacteria are controlled is poorly understood. Here, we report the identification of a two-component signaling system, composed of a histidine kinase CdgK and a response regulator CdgS, involved in cell size regulation in the filamentous, heterocyst-forming cyanobacterium Anabaena sp. PCC 7120. Inactivation of cdgK or cdgS led to reduction of cell length and width with little effect on cell growth capacity. CdgS has a GGDEF domain responsible for the synthesis of the second messenger c-di-GMP. Based on genetic and biochemical studies, we proposed a signaling pathway initiated by CdgK, leading to the phosphorylation of CdgS, and thereby an enhanced enzymatic activity for c-di-GMP synthesis of the latter. The GGDEF domain of CdgS was essential in cell size control, and the reduction of cell size observed in various mutants could be rescued by the expression of a c-di-GMP synthetase from E. coli. These results provided evidence that a minimal threshold of c-di-GMP level was required for maintaining cell size in Anabaena. IMPORTANCE Cyanobacteria are considered the first organisms to produce oxygen on Earth, and their activities shaped the evolution of our ecosystems. Cell size is an important trait fixed early in evolution, with the diversification of micro- and macrocyanobacterial species during the Great Oxidation Event. However, the genetic basis underlying cell size control in cyanobacteria was not understood. Our studies demonstrated that the CdgK-CdgS signaling pathway participates in the control of cell size, and their absence did not affect cell growth. CdgK has multiple domains susceptible to signal input, which are necessary for cell size regulation. This observation suggests that cell size in Anabaena could respond to environmental signals. These studies paved the way for genetic dissection of cell size regulation in cyanobacteria.
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Tian D, Wang C, Liu Y, Zhang Y, Caliari A, Lu H, Xia Y, Xu B, Xu J, Yomo T. Cell Sorting-Directed Selection of Bacterial Cells in Bigger Sizes Analyzed by Imaging Flow Cytometry during Experimental Evolution. Int J Mol Sci 2023; 24:ijms24043243. [PMID: 36834655 PMCID: PMC9966196 DOI: 10.3390/ijms24043243] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/10/2023] Open
Abstract
Cell morphology is an essential and phenotypic trait that can be easily tracked during adaptation and evolution to environmental changes. Thanks to the rapid development of quantitative analytical techniques for large populations of cells based on their optical properties, morphology can be easily determined and tracked during experimental evolution. Furthermore, the directed evolution of new culturable morphological phenotypes can find use in synthetic biology to refine fermentation processes. It remains unknown whether and how fast we can obtain a stable mutant with distinct morphologies using fluorescence-activated cell sorting (FACS)-directed experimental evolution. Taking advantage of FACS and imaging flow cytometry (IFC), we direct the experimental evolution of the E. coli population undergoing continuous passage of sorted cells with specific optical properties. After ten rounds of sorting and culturing, a lineage with large cells resulting from incomplete closure of the division ring was obtained. Genome sequencing highlighted a stop-gain mutation in amiC, leading to a dysfunctional AmiC division protein. The combination of FACS-based selection with IFC analysis to track the evolution of the bacteria population in real-time holds promise to rapidly select and culture new morphologies and association tendencies with many potential applications.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jian Xu
- Correspondence: (J.X.); (T.Y.); Tel.: +86-(21)-62233727 (J.X. & T.Y.)
| | - Tetsuya Yomo
- Correspondence: (J.X.); (T.Y.); Tel.: +86-(21)-62233727 (J.X. & T.Y.)
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Hossein Karimi Darvanjooghi M, Kaur K, Magdouli S, Kaur Brar S. Extracellular polymeric substances overproduction strategy in Ferroplasma acidiphilum growth for biooxidation of low-grade gold bearing ore: Role of monosaccharides. BIORESOURCE TECHNOLOGY 2023; 369:128476. [PMID: 36509301 DOI: 10.1016/j.biortech.2022.128476] [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: 10/27/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
The adhesion of microorganisms to surfaces and the affecting factors is important in biomining pretreatment. In this research, the novelty is focused on studying the monosaccharide's impact on the adaptability and adhesivity of Ferroplasma acidiphilum for oxidization of sulfide-bearing ore containing pyrite harboring 98 % of gold in its crystal lattice. d-sucrose increased EPS production with the highest amount of pyrite dissolution (69 %) as compared to the other types of monosaccharides (d-galactose and d-fructose). Addition of 0.8 wt% d-sucrose enhanced the production of ferric ions 65 % for the ore load of 20 wt% while for the addition of 0.4 wt%, the ferric ions concentration was maximum up to 95 %. The results indicated that the addition of both yeast extract and d-sucrose with the concentration of 0.4 wt% enhanced the EPS (Extracellular Polymeric Substances) biovolume fraction from 7.5 to 32.5 v/v %.
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Affiliation(s)
| | - Kamalpreet Kaur
- Research Centre of Energy, Mining, and Environment (EME), National Research Council Canada, 6100 Royalmount Ave, Montreal, QC H4P 2R2, Canada
| | - Sara Magdouli
- Department of Civil Engineering, Lassonde School of Engineering, York University, Toronto, Ontario M3J 1P3, Canada
| | - Satinder Kaur Brar
- Department of Civil Engineering, Lassonde School of Engineering, York University, Toronto, Ontario M3J 1P3, Canada.
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48
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Weber A, Gibisch M, Tyrakowski D, Cserjan-Puschmann M, Toca-Herrera JL, Striedner G. Recombinant Peptide Production Softens Escherichia coli Cells and Increases Their Size during C-Limited Fed-Batch Cultivation. Int J Mol Sci 2023; 24:2641. [PMID: 36768962 PMCID: PMC9916741 DOI: 10.3390/ijms24032641] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Stress-associated changes in the mechanical properties at the single-cell level of Escherichia coli (E. coli) cultures in bioreactors are still poorly investigated. In our study, we compared peptide-producing and non-producing BL21(DE3) cells in a fed-batch cultivation with tightly controlled process parameters. The cell growth, peptide content, and cell lysis were analysed, and changes in the mechanical properties were investigated using atomic force microscopy. Recombinant-tagged somatostatin-28 was expressed as soluble up to 197 ± 11 mg g-1. The length of both cultivated strains increased throughout the cultivation by up to 17.6%, with nearly constant diameters. The peptide-producing cells were significantly softer than the non-producers throughout the cultivation, and respective Young's moduli decreased by up to 57% over time. A minimum Young's modulus of 1.6 MPa was observed after 23 h of the fed-batch. Furthermore, an analysis of the viscoelastic properties revealed that peptide-producing BL21(DE3) appeared more fluid-like and softer than the non-producing reference. For the first time, we provide evidence that the physical properties (i.e., the mechanical properties) on the single-cell level are significantly influenced by the metabolic burden imposed by the recombinant peptide expression and C-limitation in bioreactors.
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Affiliation(s)
- Andreas Weber
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
- Institute of Biophysics, Department of Bionanosciences, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
| | - Martin Gibisch
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Daniel Tyrakowski
- Institute of Biophysics, Department of Bionanosciences, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - José L. Toca-Herrera
- Institute of Biophysics, Department of Bionanosciences, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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Liu Y, Ding C, Li X, Su D, He J. Biotic interactions contribute more than environmental factors and geographic distance to biogeographic patterns of soil prokaryotic and fungal communities. Front Microbiol 2023; 14:1134440. [PMID: 36970675 PMCID: PMC10034001 DOI: 10.3389/fmicb.2023.1134440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/21/2023] [Indexed: 03/29/2023] Open
Abstract
Recent studies have shown distinct soil microbial assembly patterns across taxonomic types, habitat types and regions, but little is known about which factors play a dominant role in soil microbial communities. To bridge this gap, we compared the differences in microbial diversity and community composition across two taxonomic types (prokaryotes and fungi), two habitat types (Artemisia and Poaceae) and three geographic regions in the arid ecosystem of northwest China. To determine the main driving factors shaping the prokaryotic and fungal community assembly, we carried out diverse analyses including null model, partial mantel test and variance partitioning analysis etc. The findings suggested that the processes of community assembly were more diverse among taxonomic categories in comparison to habitats or geographical regions. The predominant driving factor of soil microbial community assembly in arid ecosystem was biotic interactions between microorganisms, followed by environmental filtering and dispersal limitation. Network vertex, positive cohesion and negative cohesion showed the most significant correlations with prokaryotic and fungal diversity and community dissimilarity. Salinity was the major environmental variable structuring the prokaryotic community. Although prokaryotic and fungal communities were jointly regulated by the three factors, the effects of biotic interactions and environmental variables (both are deterministic processes) on the community structure of prokaryotes were stronger than that of fungi. The null model revealed that prokaryotic community assembly was more deterministic, whereas fungal community assembly was structured by stochastic processes. Taken together, these findings unravel the predominant drivers governing microbial community assembly across taxonomic types, habitat types and geographic regions and highlight the impacts of biotic interactions on disentangling soil microbial assembly mechanisms.
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Affiliation(s)
- Yu Liu
- College of Grassland, Beijing Forestry University, Beijing, China
| | - Chengxiang Ding
- Academy of Animal Husbandry and Veterinary Science, Qinghai University, Xining, Qinghai, China
| | - Xingfu Li
- Industry Development and Planning Institute, National Forestry and Grassland Administration, Beijing, China
| | - Derong Su
- College of Grassland, Beijing Forestry University, Beijing, China
- *Correspondence: Derong Su,
| | - Jing He
- College of Grassland, Beijing Forestry University, Beijing, China
- Jing He,
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50
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Wei Y, Quan F, Lan G, Wu Z, Yang C. Space Rather than Seasonal Changes Explained More of the Spatiotemporal Variation of Tropical Soil Microbial Communities. Microbiol Spectr 2022; 10:e0184622. [PMID: 36416607 PMCID: PMC9769686 DOI: 10.1128/spectrum.01846-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 11/03/2022] [Indexed: 11/24/2022] Open
Abstract
Soil microbiomes play an essential role in maintaining soil geochemical cycle and function. Although there have been some reports on the diversity patterns and drivers of the tropical forest soil microbial community, how space and seasonal changes affect spatiotemporal distribution at the regional scales are poorly understood. Based on 260 soil samples, we investigated the spatiotemporal patterns of rubber plantations and rainforest soil microbial communities across the whole of Hainan Island, China during the dry and rainy seasons. We examined soil bacterial and fungal composition and diversity and the main drivers of these microbes using Illumina sequencing and assembly. Our results revealed that the diversity (both alpha and beta) spatiotemporal variation in microbial communities is highly dependent on regional location rather than seasonal changes. For example, the site explained 28.5% and 37.2% of the variation in alpha diversity for soil bacteria and fungi, respectively, and explained 34.6% of the bacterial variance and 14.3% of the fungal variance in beta diversity. Soil pH, mean annual temperature, and mean annual precipitation were the most important factors associated with the distribution of soil microbial communities. Furthermore, we identified that variations in edaphic (e.g., soil pH) and climatic factors (e.g., mean annual temperature [MAT] and mean annual precipitation [MAP]) were mainly caused by regional sites (P < 0.001). Collectively, our work provides empirical evidence that space, rather than seasonal changes, explained more of the spatiotemporal variation of soil microbial communities in tropical forests, mediated by regional location-induced changes in climatic factors and edaphic properties. IMPORTANCE The soil microbiomes communities of the two forests were not only affected by environmental factors (e.g., edaphic and climatic factors), but also by different dominant geographic factors. In particular, our work showed that spatial variation in bacterial and fungal community composition was mainly dominated by edaphic properties (e.g., pH) and climatic factors (e.g., MAT and MAP). Moreover, the environmental factors were mainly explained by geographic location effect rather than by seasonal effect, and environmental dissimilarity significantly increased with geographic distance. In conclusion, our study provides solid empirical evidence that space rather than season explained more of the spatiotemporal variation of soil microbial communities in the tropical forest.
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Affiliation(s)
- Yaqing Wei
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou City, Hainan Province, People’s Republic of China
- Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou City, Hainan Province, People’s Republic of China
- College of Ecology and Environment, Hainan University, Haikou, China
| | - Fei Quan
- School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
- Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou City, Hainan Province, People’s Republic of China
| | - Guoyu Lan
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou City, Hainan Province, People’s Republic of China
- Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou City, Hainan Province, People’s Republic of China
| | - Zhixiang Wu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou City, Hainan Province, People’s Republic of China
- Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou City, Hainan Province, People’s Republic of China
| | - Chuan Yang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou City, Hainan Province, People’s Republic of China
- Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou City, Hainan Province, People’s Republic of China
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