1
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Jensen CNG, Pang JKY, Gottardi M, Kračun SK, Svendsen BA, Nielsen KF, Kovács ÁT, Moelbak L, Fimognari L, Husted S, Schulz A. Bacillus subtilis promotes plant phosphorus (P) acquisition through P solubilization and stimulation of root and root hair growth. Physiol Plant 2024; 176:e14338. [PMID: 38740528 DOI: 10.1111/ppl.14338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/03/2024] [Accepted: 04/12/2024] [Indexed: 05/16/2024]
Abstract
Bacteria can be applied as biofertilizers to improve crop growth in phosphorus (P)-limited conditions. However, their mode of action in a soil environment is still elusive. We used the strain ALC_02 as a case study to elucidate how Bacillus subtilis affects dwarf tomato cultivated in soil-filled rhizoboxes over time. ALC_02 improved plant P acquisition by increasing the size and P content of P-limited plants. We assessed three possible mechanisms, namely root growth stimulation, root hair elongation, and solubilization of soil P. ALC_02 produced auxin, and inoculation with ALC_02 promoted root growth. ALC_02 promoted root hair elongation as the earliest observed response and colonized root hairs specifically. Root and root hair growth stimulation was associated with a subsequent increase in plant P content, indicating that a better soil exploration by the root system improved plant P acquisition. Furthermore, ALC_02 affected the plant-available P content in sterilized soil differently over time and released P from native P pools in the soil. Collectively, ALC_02 exhibited all three mechanisms in a soil environment. To our knowledge, bacterial P biofertilizers have not been reported to colonize and elongate root hairs in the soil so far, and we propose that these traits contribute to the overall effect of ALC_02. The knowledge gained in this research can be applied in the future quest for bacterial P biofertilizers, where we recommend assessing all three parameters, not only root growth and P solubilization, but also root hair elongation. This will ultimately support the development of sustainable agricultural practices.
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Affiliation(s)
- Camilla Niketa Gadomska Jensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- Plant Health Innovation, Novonesis A/S, Taastrup, Denmark
| | - Janet Ka Yan Pang
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | | | | | | | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Lars Moelbak
- Plant Health Innovation, Novonesis A/S, Taastrup, Denmark
| | | | - Søren Husted
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Alexander Schulz
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
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2
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García-Bayona L, Said N, Coyne MJ, Flores K, Elmekki NM, Sheahan ML, Camacho AG, Hutt K, Yildiz FH, Kovács ÁT, Waldor MK, Comstock LE. A pervasive large conjugative plasmid mediates multispecies biofilm formation in the intestinal microbiota increasing resilience to perturbations. bioRxiv 2024:2024.04.29.590671. [PMID: 38746121 PMCID: PMC11092513 DOI: 10.1101/2024.04.29.590671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Although horizontal gene transfer is pervasive in the intestinal microbiota, we understand only superficially the roles of most exchanged genes and how the mobile repertoire affects community dynamics. Similarly, little is known about the mechanisms underlying the ability of a community to recover after a perturbation. Here, we identified and functionally characterized a large conjugative plasmid that is one of the most frequently transferred elements among Bacteroidales species and is ubiquitous in diverse human populations. This plasmid encodes both an extracellular polysaccharide and fimbriae, which promote the formation of multispecies biofilms in the mammalian gut. We use a hybridization-based approach to visualize biofilms in clarified whole colon tissue with unprecedented 3D spatial resolution. These biofilms increase bacterial survival to common stressors encountered in the gut, increasing strain resiliency, and providing a rationale for the plasmid's recent spread and high worldwide prevalence.
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3
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Xu X, Kovács ÁT. How to identify and quantify the members of the Bacillus genus? Environ Microbiol 2024; 26:e16593. [PMID: 38383138 DOI: 10.1111/1462-2920.16593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024]
Abstract
Members of the Bacillus genus are widely distributed throughout natural environments and have been studied for decades among others for their physiology, genetics, ecological functions, and applications. However, despite its prevalence in nature, the characterization and classification of Bacillus remain challenging due to its complex and ever-evolving taxonomic framework. This review addresses the current state of the Bacillus taxonomic landscape and summarizes the critical points in the development of Bacillus phylogeny. With a clear view of Bacillus phylogeny as a foundation, we subsequently review the methodologies applied in identifying and quantifying Bacillus, while also discussing their respective advantages and disadvantages.
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Affiliation(s)
- Xinming Xu
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ákos T Kovács
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
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4
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Jensen CNG, Pang JKY, Hahn CM, Gottardi M, Husted S, Moelbak L, Kovács ÁT, Fimognari L, Schulz A. Differential influence of Bacillus subtilis strains on Arabidopsis root architecture through common and distinct plant hormonal pathways. Plant Sci 2024; 339:111936. [PMID: 38042415 DOI: 10.1016/j.plantsci.2023.111936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/28/2023] [Indexed: 12/04/2023]
Abstract
Plant growth-promoting microbes (PGPM) can enhance crop yield and health, but knowledge of their mode-of-action is limited. We studied the influence of two Bacillus subtilis strains, the natural isolate ALC_02 and the domesticated 168 Gö, on Arabidopsis and hypothesized that they modify the root architecture by modulating hormone transport or signaling. Both bacteria promoted increase of shoot and root surface area in vitro, but through different root anatomical traits. Mutant plants deficient in auxin transport or signaling responded less to the bacterial strains than the wild-type, and application of the auxin transport inhibitor NPA strongly reduced the influence of the strains. Both bacteria produced auxin and enhanced shoot auxin levels in DR5::GUS reporter plants. Accordingly, most of the beneficial effects of the strains were dependent on functional auxin transport and signaling, while only 168 Gö depended on functional ethylene signaling. As expected, only ALC_02 stimulated plant growth in soil, unlike 168 Gö that was previously reported to have reduced biofilms. Collectively, the results highlight that B. subtilis strains can have strikingly different plant growth-promoting properties, dependent on what experimental setup they are tested in, and the importance of choosing the right PGPM for a desired root phenotype.
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Affiliation(s)
- Camilla Niketa Gadomska Jensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark; Plant Health Innovation, Chr-Hansen A/S, Taastrup, Denmark
| | - Janet Ka Yan Pang
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Charlotte Marie Hahn
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Søren Husted
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Lars Moelbak
- Plant Health Innovation, Chr-Hansen A/S, Taastrup, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Alexander Schulz
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark.
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5
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Lyng M, Jørgensen JPB, Schostag MD, Jarmusch SA, Aguilar DKC, Lozano-Andrade CN, Kovács ÁT. Competition for iron shapes metabolic antagonism between Bacillus subtilis and Pseudomonas marginalis. ISME J 2024; 18:wrad001. [PMID: 38365234 PMCID: PMC10811728 DOI: 10.1093/ismejo/wrad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 02/18/2024]
Abstract
Siderophores have long been implicated in sociomicrobiology as determinants of bacterial interrelations. For plant-associated genera, like Bacillus and Pseudomonas, siderophores are well known for their biocontrol functions. Here, we explored the functional role of the Bacillus subtilis siderophore bacillibactin (BB) in an antagonistic interaction with Pseudomonas marginalis. The presence of BB strongly influenced the outcome of the interaction in an iron-dependent manner. The BB producer B. subtilis restricts colony spreading of P. marginalis by repressing the transcription of histidine kinase-encoding gene gacS, thereby abolishing production of secondary metabolites such as pyoverdine and viscosin. By contrast, lack of BB restricted B. subtilis colony growth. To explore the specificity of the antagonism, we cocultured B. subtilis with a collection of fluorescent Pseudomonas spp. and found that the Bacillus-Pseudomonas interaction is conserved, expanding our understanding of the interplay between two of the most well-studied genera of soil bacteria.
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Affiliation(s)
- Mark Lyng
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Johan P B Jørgensen
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Morten D Schostag
- Bacterial Ecophysiology & Biotechnology, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Scott A Jarmusch
- Natural Product Discovery, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Diana K C Aguilar
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Carlos N Lozano-Andrade
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
- Institute of Biology Leiden, Leiden University, Leiden 2333 BE, The Netherlands
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6
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Kovács ÁT. Plant cell wall component induced bacterial development. Trends Microbiol 2024; 32:1-3. [PMID: 37838589 DOI: 10.1016/j.tim.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/03/2023] [Indexed: 10/16/2023]
Abstract
Plant-microbiome functioning depends on intricate signaling pathways including plant-derived excretions that induce microbial gene expression. Marc Ongena and his team (Boubsi et al.) dissect how the pectin backbone homogalacturonan promotes bacterial differentiation programs of Bacillus velezensis, potentially facilitating its establishment in the rhizosphere.
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Affiliation(s)
- Ákos T Kovács
- Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands.
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7
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Sun X, Xie J, Zheng D, Xia R, Wang W, Xun W, Huang Q, Zhang R, Kovács ÁT, Xu Z, Shen Q. Metabolic interactions affect the biomass of synthetic bacterial biofilm communities. mSystems 2023; 8:e0104523. [PMID: 37971263 PMCID: PMC10734490 DOI: 10.1128/msystems.01045-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Co-occurrence network analysis is an effective tool for predicting complex networks of microbial interactions in the natural environment. Using isolates from a rhizosphere, we constructed multi-species biofilm communities and investigated co-occurrence patterns between microbial species in genome-scale metabolic models and in vitro experiments. According to our results, metabolic exchanges and resource competition may partially explain the co-occurrence network analysis results found in synthetic bacterial biofilm communities.
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Affiliation(s)
- Xinli Sun
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing, Jiangsu, China
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jiyu Xie
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing, Jiangsu, China
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Daoyue Zheng
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Riyan Xia
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Wei Wang
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Weibing Xun
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Qiwei Huang
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Ruifu Zhang
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Ákos T. Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
| | - Zhihui Xu
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Qirong Shen
- Key lab of organic-based fertilizers of China and Jiangsu provincial key lab for solid organic waste utilization, Nanjing Agricultural University, Nanjing, Jiangsu, China
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8
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Kovács ÁT. Correction: Diversification during cross-kingdom microbial experimental evolution. ISME J 2023; 17:2458. [PMID: 37968505 PMCID: PMC10689809 DOI: 10.1038/s41396-023-01551-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Affiliation(s)
- Ákos T Kovács
- Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands.
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9
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Xu X, Nielsen LJD, Song L, Maróti G, Strube ML, Kovács ÁT. Enhanced specificity of Bacillus metataxonomics using a tuf-targeted amplicon sequencing approach. ISME Commun 2023; 3:126. [PMID: 38012258 PMCID: PMC10682494 DOI: 10.1038/s43705-023-00330-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 11/01/2023] [Accepted: 11/08/2023] [Indexed: 11/29/2023]
Abstract
Bacillus species are ubiquitous in nature and have tremendous application potential in agriculture, medicine, and industry. However, the individual species of this genus vary widely in both ecological niches and functional phenotypes, which, hence, requires accurate classification of these bacteria when selecting them for specific purposes. Although analysis of the 16S rRNA gene has been widely used to disseminate the taxonomy of most bacterial species, this gene fails proper classification of Bacillus species. To circumvent this restriction, we designed novel primers and optimized them to allow exact species resolution of Bacillus species in both synthetic and natural communities using high-throughput amplicon sequencing. The primers designed for the tuf gene were not only specific for the Bacillus genus but also sufficiently discriminated species both in silico and in vitro in a mixture of 11 distinct Bacillus species. Investigating the primers using a natural soil sample, 13 dominant species were detected including Bacillus badius, Bacillus velezensis, and Bacillus mycoides as primary members, neither of which could be distinguished with 16S rRNA sequencing. In conclusion, a set of high-throughput primers were developed which allows unprecedented species-level identification of Bacillus species and aids the description of the ecological distribution of Bacilli in various natural environment.
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Affiliation(s)
- Xinming Xu
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
- Institute of Biology Leiden, Leiden University, 2333 BE, Leiden, The Netherlands
| | - Lasse Johan Dyrbye Nielsen
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Lijie Song
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
- BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, ELKH, 6726, Szeged, Hungary
| | - Mikael Lenz Strube
- Bacterial Ecophysiology and Biotechnology Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark.
- Institute of Biology Leiden, Leiden University, 2333 BE, Leiden, The Netherlands.
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10
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Hu G, Wang Y, Liu X, Strube ML, Wang B, Kovács ÁT. Species and condition shape the mutational spectrum in experimentally evolved biofilms. mSystems 2023; 8:e0054823. [PMID: 37768063 PMCID: PMC10654089 DOI: 10.1128/msystems.00548-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 08/11/2023] [Indexed: 09/29/2023] Open
Abstract
IMPORTANCE Biofilm formation is a vital factor for the survival and adaptation of bacteria in diverse environmental niches. Experimental evolution combined with the advancement of whole-population genome sequencing provides us a powerful tool to understand the genomic dynamic of evolutionary adaptation to different environments, such as during biofilm development. Previous studies described the genetic and phenotypic changes of selected clones from experimentally evolved Bacillus thuringiensis and Bacillus subtilis that were adapted under abiotic and biotic biofilm conditions. However, the full understanding of the dynamic evolutionary landscapes was lacking. Furthermore, the differences and similarities of adaptive mechanisms in B. thuringiensis and B. subtilis were not identified. To overcome these limitations, we performed longitudinal whole-population genome sequencing to study the underlying genetic dynamics at high resolution. Our study provides the first comprehensive mutational landscape of two bacterial species' biofilms that is adapted to an abiotic and biotic surface.
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Affiliation(s)
- Guohai Hu
- China National GeneBank, BGI, Shenzhen, China
- BGI Research, Shenzhen, China
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Yue Wang
- China National GeneBank, BGI, Shenzhen, China
- BGI Research, Shenzhen, China
- BGI Research, Beijing, China
| | - Xin Liu
- China National GeneBank, BGI, Shenzhen, China
- BGI Research, Shenzhen, China
- BGI Research, Beijing, China
| | - Mikael Lenz Strube
- Bacterial Ecophysiology and Biotechnology Group, DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Bo Wang
- China National GeneBank, BGI, Shenzhen, China
- BGI Research, Shenzhen, China
- Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, BGI Research, Shenzhen, China
| | - Ákos T. Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark
- Institute of Biology, Leiden University, Leiden, The Netherlands
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11
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Lozano-Andrade CN, Nogueira CG, Henriksen NNSE, Wibowo M, Jarmusch SA, Kovács ÁT. Establishment of a transparent soil system to study Bacillus subtilis chemical ecology. ISME Commun 2023; 3:110. [PMID: 37838789 PMCID: PMC10576751 DOI: 10.1038/s43705-023-00318-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/21/2023] [Accepted: 10/05/2023] [Indexed: 10/16/2023]
Abstract
Bacterial secondary metabolites are structurally diverse molecules that drive microbial interaction by altering growth, cell differentiation, and signaling. Bacillus subtilis, a Gram-positive soil-dwelling bacterium, produces a wealth of secondary metabolites, among them, lipopeptides have been vastly studied by their antimicrobial, antitumor, and surfactant activities. However, the natural functions of secondary metabolites in the lifestyles of the producing organism remain less explored under natural conditions, i.e. in soil. Here, we describe a hydrogel-based transparent soil system to investigate B. subtilis chemical ecology under controllable soil-like conditions. The transparent soil matrix allows the growth of B. subtilis and other isolates gnotobiotically and under nutrient-controlled conditions. Additionally, we show that transparent soil allows the detection of lipopeptides production and dynamics by HPLC-MS, and MALDI-MS imaging, along with fluorescence imaging of 3-dimensional bacterial assemblages. We anticipate that this affordable and highly controllable system will promote bacterial chemical ecology research and help to elucidate microbial interactions driven by secondary metabolites.
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Affiliation(s)
| | - Carla G Nogueira
- DTU Bioengineering, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | | | - Mario Wibowo
- DTU Bioengineering, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Scott A Jarmusch
- DTU Bioengineering, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Ákos T Kovács
- DTU Bioengineering, Technical University of Denmark, 2800, Kgs Lyngby, Denmark.
- Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands.
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12
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Kovács ÁT. Colony morphotype diversification as a signature of bacterial evolution. Microlife 2023; 4:uqad041. [PMID: 37901115 PMCID: PMC10608940 DOI: 10.1093/femsml/uqad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 10/05/2023] [Accepted: 10/07/2023] [Indexed: 10/31/2023]
Abstract
The appearance of colony morphotypes is a signature of genetic diversification in evolving bacterial populations. Colony structure highly depends on the cell-cell interactions and polymer production that are adjusted during evolution in an environment that allows the development of spatial structures. Nucci and colleagues describe the emergence of a rough and dry morphotype of a noncapsulated Klebsiella variicola strain during a laboratory evolution study, resembling genetic changes observed in clinical isolates.
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Affiliation(s)
- Ákos T Kovács
- Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
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13
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Danevčič T, Spacapan M, Dragoš A, Kovács ÁT, Mandic-Mulec I. DegQ is an important policing link between quorum sensing and regulated adaptative traits in Bacillus subtilis. Microbiol Spectr 2023; 11:e0090823. [PMID: 37676037 PMCID: PMC10581247 DOI: 10.1128/spectrum.00908-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/26/2023] [Indexed: 09/08/2023] Open
Abstract
Quorum sensing (QS) is a widespread bacterial communication system that controls important adaptive traits in a cell density-dependent manner. However, mechanisms by which QS-regulated traits are linked within the cell and mechanisms by which these links affect adaptation are not well understood. In this study, Bacillus subtilis was used as a model bacterium to investigate the link between the ComQXPA QS system, DegQ, surfactin and protease production in planktonic and biofilm cultures. The work tests two alternative hypotheses predicting that hypersensitivity of the QS signal-deficient mutant (comQ::kan) to exogenously added ComX, resulting in increased surfactin production, is linked to an additional genetic locus, or alternatively, to overexpression of the ComX receptor ComP. Results are in agreement with the first hypothesis and show that the P srfAA hypersensitivity of the comQ::kan mutant is linked to a 168 strain-specific mutation in the P degQ region. Hence, the markerless ΔcomQ mutant lacking this mutation is not overresponsive to ComX. Such hyper-responsiveness is specific for the P srfAA and not detected in another ComX-regulated promoter, the P aprE , which is under the positive control by DegQ. Our results suggest that DegQ by exerting differential effect on P srfAA and P aprE acts as a policing mechanism and the intracellular link, which guards the cell from an overinvestment into surfactin production. IMPORTANCE DegQ levels are known to regulate surfactin synthesis and extracellular protease production, and DegQ is under the control of the ComX-dependent QS. DegQ also serves as an important policing link between these QS-regulated processes, preventing overinvestment in these costly processes. This work highlights the importance of DegQ, which acts as the intracellular link between ComX production and the response by regulating extracellular degradative enzyme synthesis and surfactin production.
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Affiliation(s)
- Tjaša Danevčič
- Department of Microbiology, Chair of microbial ecology and physiology, University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Mihael Spacapan
- Department of Microbiology, Chair of microbial ecology and physiology, University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Anna Dragoš
- Department of Microbiology, Chair of microbial ecology and physiology, University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Ákos T. Kovács
- Department of Biotechnology and Biomedicine, Bacterial Interactions and Evolution Group, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ines Mandic-Mulec
- Department of Microbiology, Chair of microbial ecology and physiology, University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
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14
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Kovács ÁT. Diversification during cross-kingdom microbial experimental evolution. ISME J 2023; 17:1355-1357. [PMID: 37524911 PMCID: PMC10432481 DOI: 10.1038/s41396-023-01479-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 07/07/2023] [Accepted: 07/11/2023] [Indexed: 08/02/2023]
Affiliation(s)
- Ákos T Kovács
- Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands.
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15
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Kovács ÁT. Plant-microbe interactions: Plant-exuded myo-inositol attracts specific bacterial taxa. Curr Biol 2023; 33:R825-R827. [PMID: 37552953 DOI: 10.1016/j.cub.2023.06.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Plants exude a plethora of metabolites that transform the microbiome composition. Initiated from genome-wide association studies of either a plant or a bacterium, two new studies dissect the impact of plant-secreted myo-inositol on recruitment of certain bacterial taxa by Arabidopsis.
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Affiliation(s)
- Ákos T Kovács
- Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands.
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16
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Sartor F, Xu X, Popp T, Dodd AN, Kovács ÁT, Merrow M. The circadian clock of the bacterium B. subtilis evokes properties of complex, multicellular circadian systems. Sci Adv 2023; 9:eadh1308. [PMID: 37540742 PMCID: PMC10403212 DOI: 10.1126/sciadv.adh1308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 07/05/2023] [Indexed: 08/06/2023]
Abstract
Circadian clocks are pervasive throughout nature, yet only recently has this adaptive regulatory program been described in nonphotosynthetic bacteria. Here, we describe an inherent complexity in the Bacillus subtilis circadian clock. We find that B. subtilis entrains to blue and red light and that circadian entrainment is separable from masking through fluence titration and frequency demultiplication protocols. We identify circadian rhythmicity in constant light, consistent with the Aschoff's rule, and entrainment aftereffects, both of which are properties described for eukaryotic circadian clocks. We report that circadian rhythms occur in wild isolates of this prokaryote, thus establishing them as a general property of this species, and that its circadian system responds to the environment in a complex fashion that is consistent with multicellular eukaryotic circadian systems.
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Affiliation(s)
- Francesca Sartor
- Institute of Medical Psychology, Medical Faculty, LMU Munich, Munich, Germany
| | - Xinming Xu
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Tanja Popp
- Institute of Medical Psychology, Medical Faculty, LMU Munich, Munich, Germany
| | - Antony N. Dodd
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Ákos T. Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Martha Merrow
- Institute of Medical Psychology, Medical Faculty, LMU Munich, Munich, Germany
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17
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Hu G, Wang Y, Blake C, Nordgaard M, Liu X, Wang B, Kovács ÁT. Parallel genetic adaptation of Bacillus subtilis to different plant species. Microb Genom 2023; 9:mgen001064. [PMID: 37466402 PMCID: PMC10438812 DOI: 10.1099/mgen.0.001064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
Plant growth-promoting rhizobacteria benefit plants by stimulating their growth or protecting them against phytopathogens. Rhizobacteria must colonize and persist on plant roots to exert their benefits. However, little is known regarding the processes by which rhizobacteria adapt to different plant species, or behave under alternating host plant regimes. Here, we used experimental evolution and whole-population whole-genome sequencing to analyse how Bacillus subtilis evolves on Arabidopsis thaliana and tomato seedlings, and under an alternating host plant regime, in a static hydroponic setup. We observed parallel evolution across multiple levels of biological organization in all conditions, which was greatest for the two heterogeneous, multi-resource, spatially structured environments at the genetic level. Species-specific adaptation at the genetic level was also observed, possibly caused by the selection stress imposed by different host plants. Furthermore, a trade-off between motility and biofilm development was supported by mutational changes in motility- and biofilm-related genes. Finally, we identified several condition-specific and common targeted genes in different environments by comparing three different B. subtilis biofilm adaptation settings. The results demonstrate a common evolutionary pattern when B. subtilis is adapting to the plant rhizosphere in similar conditions, and reveal differences in genetic mechanisms between different host plants. These findings will likely support strain improvements for sustainable agriculture.
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Affiliation(s)
- Guohai Hu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, PR China
- BGI-Shenzhen, Shenzhen 518083, PR China
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Yue Wang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, PR China
- BGI-Shenzhen, Shenzhen 518083, PR China
- BGI-Beijing, Beijing 102601, PR China
| | - Christopher Blake
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Mathilde Nordgaard
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Xin Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, PR China
- BGI-Shenzhen, Shenzhen 518083, PR China
- BGI-Beijing, Beijing 102601, PR China
| | - Bo Wang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, PR China
- BGI-Shenzhen, Shenzhen 518083, PR China
- Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, BGI Shenzhen, 518083 Shenzhen, PR China
| | - Ákos T. Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800 Lyngby, Denmark
- Institute of Biology Leiden, Leiden University, 2333BE Leiden, Netherlands
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18
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Gallegos-Monterrosa R, Kovács ÁT. Phenotypic plasticity: The role of a phosphatase family Rap in the genetic regulation of Bacilli. Mol Microbiol 2023. [PMID: 37042030 DOI: 10.1111/mmi.15060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/23/2023] [Accepted: 03/26/2023] [Indexed: 04/13/2023]
Abstract
In the last two decades, an increasing number of bacterial species have been recognized that are able to generate a phenotypically diverse population that shares an identical genotype. This ability is dependent on a complex genetic regulatory network that includes cellular and environmental signals, as well as stochastic elements. Among Bacilli, a broadly distributed family of Rap (Response-regulator aspartyl phosphate) phosphatases is known to modulate the function of the main phenotypic heterogeneity regulators by controlling their phosphorylation. Even more, their related extracellular Phr (Phosphatase regulator) peptides function as signals, creating a cell-cell communication network that regulates the phenotypic development of the entire population. In this review, we examine the role that the Rap phosphatases and their Phr peptides play in the regulation of Bacillus subtilis phenotypic differentiation, and in other members of the Bacillus genus. We also highlight the contribution of these regulatory elements to the fitness of bacterial cells and mobile genetic elements, for example, prophages and conjugative vectors.
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Affiliation(s)
- Ramses Gallegos-Monterrosa
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, C.P. 62210, Cuernavaca, Morelos, Mexico
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
- Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands
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19
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Lyng M, Kovács ÁT. Frenemies of the soil: Bacillus and Pseudomonas interspecies interactions. Trends Microbiol 2023:S0966-842X(23)00050-1. [PMID: 36878770 DOI: 10.1016/j.tim.2023.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 03/07/2023]
Abstract
Bacillus and Pseudomonas ubiquitously occur in natural environments and are two of the most intensively studied bacterial genera in the soil. They are often coisolated from environmental samples, and as a result, several studies have experimentally cocultured bacilli and pseudomonads to obtain emergent properties. Even so, the general interaction between members of these genera is virtually unknown. In the past decade, data on interspecies interactions between natural isolates of Bacillus and Pseudomonas has become more detailed, and now, molecular studies permit mapping of the mechanisms behind their pairwise ecology. This review addresses the current knowledge about microbe-microbe interactions between strains of Bacillus and Pseudomonas and discusses how we can attempt to generalize the interaction on a taxonomic and molecular level.
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Affiliation(s)
- Mark Lyng
- Bacterial Interactions and Evolution group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark; Institute of Biology, Leiden University, Leiden, The Netherlands.
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20
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Jautzus T, van Gestel J, Kovács ÁT. Complex extracellular biology drives surface competition during colony expansion in Bacillus subtilis. ISME J 2022; 16:2320-2328. [PMID: 35790818 PMCID: PMC9477810 DOI: 10.1038/s41396-022-01279-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/13/2022] [Accepted: 06/20/2022] [Indexed: 04/29/2023]
Abstract
Many bacteria grow on surfaces in nature, where they form cell collectives that compete for space. Within these collectives, cells often secrete molecules that benefit surface spreading by, for example, reducing surface tension or promoting filamentous growth. Although we have a detailed understanding of how these molecules are produced, much remains unknown about their role in surface competition. Here we examine sliding motility in Bacillus subtilis and compare how secreted molecules, essential for sliding, affect intraspecific cooperation and competition on a surface. We specifically examine (i) the lipopeptide surfactin, (ii) the hydrophobin protein BslA, and (iii) exopolysaccharides (EPS). We find that these molecules have a distinct effect on surface competition. Whereas surfactin acts like a common good, which is costly to produce and benefits cells throughout the surface, BslA and EPS are cost-free and act locally. Accordingly, surfactin deficient mutants can exploit the wild-type strain in competition for space, while BslA and EPS mutants cannot. Supported by a mathematical model, we show that three factors are important in predicting the outcome of surface competition: the costs of molecule synthesis, the private benefits of molecule production, and the diffusion rate. Our results underscore the intricate extracellular biology that can drive bacterial surface competition.
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Affiliation(s)
- Theresa Jautzus
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Jordi van Gestel
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Ákos T Kovács
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, 07743, Jena, Germany.
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
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21
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Jakab Á, Kovács F, Balla N, Tóth Z, Ragyák Á, Sajtos Z, Csillag K, Nagy-Köteles C, Nemes D, Bácskay I, Pócsi I, Majoros L, Kovács ÁT, Kovács R. Physiological and transcriptional profiling of surfactin exerted antifungal effect against Candida albicans. Biomed Pharmacother 2022; 152:113220. [PMID: 35671583 DOI: 10.1016/j.biopha.2022.113220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 11/28/2022] Open
Abstract
Given the risk of Candida albicans overgrowth in the gut, novel complementary therapies should be developed to reduce fungal dominancy. This study highlights the antifungal characteristics of a Bacillus subtilis-derived secondary metabolite, surfactin with high potential against C. albicans. Surfactin inhibited the growth of C. albicans following a 1-hour exposure, in addition to reduced adhesion and morphogenesis. Specifically, surfactin did not affect the level of reactive oxygen species but increased the level of reduced glutathione. Surprisingly, ethanol production was increased following 2 h of surfactin exposure. Surfactin treatment caused a significant reduction in intracellular iron, manganese and zinc content compared to control cells, whereas the level of copper was not affected. Alongside these physiological properties, surfactin also enhanced fluconazole efficacy. To gain detailed insights into the surfactin-related effects on C. albicans, genome-wide gene transcription analysis was performed. Surfactin treatment resulted in 1390 differentially expressed genes according to total transcriptome sequencing (RNA-Seq). Of these, 773 and 617 genes with at least a 1.5-fold increase or decrease in transcription, respectively, were selected for detailed investigation. Several genes involved in morphogenesis or related to metabolism (e.g., glycolysis, ethanol and fatty acid biosynthesis) were down-regulated. Moreover, surfactin decreased the expression of ERG1, ERG3, ERG9, ERG10 and ERG11 involved in ergosterol synthesis, whereas genes associated with ribosome biogenesis and iron metabolism and drug transport-related genes were up-regulated. Our data demonstrate that surfactin significantly influences the physiology and gene transcription of C. albicans, and could contribute to the development of a novel innovative complementary therapy.
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Affiliation(s)
- Ágnes Jakab
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary; Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Fruzsina Kovács
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Doctoral School of Pharmaceutical Sciences, University of Debrecen, Debrecen, Hungary
| | - Noémi Balla
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Doctoral School of Pharmaceutical Sciences, University of Debrecen, Debrecen, Hungary
| | - Zoltán Tóth
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Doctoral School of Pharmaceutical Sciences, University of Debrecen, Debrecen, Hungary
| | - Ágota Ragyák
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary; Department of Inorganic and Analytical Chemistry, Agilent Atomic Spectroscopy Partner Laboratory, University of Debrecen, Debrecen, Hungary
| | - Zsófi Sajtos
- Department of Inorganic and Analytical Chemistry, Agilent Atomic Spectroscopy Partner Laboratory, University of Debrecen, Debrecen, Hungary
| | - Kinga Csillag
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Csaba Nagy-Köteles
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Dániel Nemes
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Debrecen, Debrecen, Hungary
| | - Ildikó Bácskay
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Debrecen, Debrecen, Hungary
| | - István Pócsi
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - László Majoros
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Renátó Kovács
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Faculty of Pharmacy, University of Debrecen, Debrecen, Hungary.
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22
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Lyng M, Kovács ÁT. Microbial ecology: Metabolic heterogeneity and the division of labor in multicellular structures. Curr Biol 2022; 32:R771-R774. [PMID: 35882195 DOI: 10.1016/j.cub.2022.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Many bacterial species are capable of differentiating to create phenotypic heterogeneity. Using the aggregate-forming marine bacterium Vibrio splendidus, a new study reveals how this organism differentiates to form spherical structures with a motile, carbon-storing core and a non-motile shell.
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Affiliation(s)
- Mark Lyng
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark.
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23
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Nordgaard M, Blake C, Maróti G, Hu G, Wang Y, Strube ML, Kovács ÁT. Experimental evolution of Bacillus subtilis on Arabidopsis thaliana roots reveals fast adaptation and improved root colonization. iScience 2022; 25:104406. [PMID: 35663012 PMCID: PMC9157203 DOI: 10.1016/j.isci.2022.104406] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/22/2022] [Accepted: 05/05/2022] [Indexed: 12/16/2022] Open
Abstract
Bacillus subtilis is known to promote plant growth and protect plants against disease. B. subtilis rapidly adapts to Arabidopsis thaliana root colonization, as evidenced by improved root colonizers already after 12 consecutive transfers between seedlings in a hydroponic setup. Re-sequencing of single evolved isolates and endpoint populations revealed mutations in genes related to different bacterial traits, in accordance with evolved isolates displaying increased root colonization associated with robust biofilm formation in response to the plant polysaccharide xylan and impaired motility. Interestingly, evolved isolates suffered a fitness disadvantage in a non-selective environment, demonstrating an evolutionary cost of adaptation to the plant root. Finally, increased root colonization by an evolved isolate was also demonstrated in the presence of resident soil microbes. Our findings highlight how a plant growth-promoting rhizobacterium rapidly adapts to an ecologically relevant environment and reveal evolutionary consequences that are fundamental to consider when evolving strains for biocontrol purposes. Bacillus subtilis shows fast adaptation to Arabidopsis thaliana roots in a hydroponic setup Evolved isolates exhibit robust biofilms in response to xylan and impaired motility Adaptation to A. thaliana roots is accompanied by an evolutionary cost An evolved isolate shows higher root colonization in the presence of soil bacteria
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Affiliation(s)
- Mathilde Nordgaard
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Christopher Blake
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network (ELKH), 6726 Szeged, Hungary
| | - Guohai Hu
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.,China National GeneBank, BGI-Shenzhen, 518120 Shenzhen, China
| | - Yue Wang
- China National GeneBank, BGI-Shenzhen, 518120 Shenzhen, China.,BGI-Beijing, BGI-Shenzhen, 100101 Beijing, China
| | - Mikael Lenz Strube
- Bacterial Ecophysiology and Biotechnology Group, DTU Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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24
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Kjeldgaard B, Neves AR, Fonseca C, Kovács ÁT, Domínguez-Cuevas P. Quantitative High-Throughput Screening Methods Designed for Identification of Bacterial Biocontrol Strains with Antifungal Properties. Microbiol Spectr 2022; 10:e0143321. [PMID: 35254137 PMCID: PMC9045326 DOI: 10.1128/spectrum.01433-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 02/07/2022] [Indexed: 01/19/2023] Open
Abstract
Large screens of bacterial strain collections to identify potential biocontrol agents often are time-consuming and costly and fail to provide quantitative results. In this study, we present two quantitative and high-throughput methods to assess the inhibitory capacity of bacterial biocontrol candidates against fungal phytopathogens. One method measures the inhibitory effect of bacterial culture supernatant components on the fungal growth, while the other accounts for direct interaction between growing bacteria and the fungus by cocultivating the two organisms. The antagonistic supernatant method quantifies the culture components' antifungal activity by calculating the cumulative impact of supernatant addition relative to the growth of a nontreated fungal control, while the antagonistic cocultivation method identifies the minimal bacterial cell concentration required to inhibit fungal growth by coinoculating fungal spores with bacterial culture dilution series. Thereby, both methods provide quantitative measures of biocontrol efficiency and allow prominent fungal inhibitors to be distinguished from less effective strains. The combination of the two methods sheds light on the types of inhibition mechanisms and provides the basis for further mode-of-action studies. We demonstrate the efficacy of the methods using Bacillus spp. with different levels of antifungal activities as model antagonists and quantify their inhibitory potencies against classic plant pathogens. IMPORTANCE Fungal phytopathogens are responsible for tremendous agricultural losses on an annual basis. While microbial biocontrol agents represent a promising solution to the problem, there is a growing need for high-throughput methods to evaluate and quantify inhibitory properties of new potential biocontrol agents for agricultural application. In this study, we present two high-throughput and quantitative fungal inhibition methods that are suitable for commercial biocontrol screening.
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Affiliation(s)
- Bodil Kjeldgaard
- Discovery, R&D, Chr. Hansen A/S, Hoersholm, Denmark
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | | | - Ákos T. Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
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25
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Lin Y, Xu X, Maróti G, Strube ML, Kovács ÁT. Adaptation and phenotypic diversification of Bacillus thuringiensis biofilm are accompanied by fuzzy spreader morphotypes. NPJ Biofilms Microbiomes 2022; 8:27. [PMID: 35418164 PMCID: PMC9007996 DOI: 10.1038/s41522-022-00292-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 03/19/2022] [Indexed: 11/12/2022] Open
Abstract
Bacillus cereus group (Bacillus cereus sensu lato) has a diverse ecology, including various species that produce biofilms on abiotic and biotic surfaces. While genetic and morphological diversification enables the adaptation of multicellular communities, this area remains largely unknown in the Bacillus cereus group. In this work, we dissected the experimental evolution of Bacillus thuringiensis 407 Cry- during continuous recolonization of plastic beads. We observed the evolution of a distinct colony morphotype that we named fuzzy spreader (FS) variant. Most multicellular traits of the FS variant displayed higher competitive ability versus the ancestral strain, suggesting an important role for diversification in the adaptation of B. thuringiensis to the biofilm lifestyle. Further genetic characterization of FS variant revealed the disruption of a guanylyltransferase gene by an insertion sequence (IS) element, which could be similarly observed in the genome of a natural isolate. The evolved FS and the deletion mutant in the guanylyltransferase gene (Bt407ΔrfbM) displayed similarly altered aggregation and hydrophobicity compared to the ancestor strain, suggesting that the adaptation process highly depends on the physical adhesive forces.
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Affiliation(s)
- Yicen Lin
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Xinming Xu
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, ELKH, 6726, Szeged, Hungary
| | - Mikael Lenz Strube
- Bacterial Ecophysiology and Biotechnology Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark.
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26
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Lin Y, Briandet R, Kovács ÁT. Bacillus cereus sensu lato biofilm formation and its ecological importance. Biofilm 2022; 4:100070. [PMID: 35243332 PMCID: PMC8861577 DOI: 10.1016/j.bioflm.2022.100070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/04/2022] [Accepted: 02/05/2022] [Indexed: 12/20/2022] Open
Abstract
Biofilm formation is a ubiquitous process of bacterial communities that enables them to survive and persist in various environmental niches. The Bacillus cereus group includes phenotypically diversified species that are widely distributed in the environment. Often, B. cereus is considered a soil inhabitant, but it is also commonly isolated from plant roots, nematodes, and food products. Biofilms differ in their architecture and developmental processes, reflecting adaptations to specific niches. Importantly, some B. cereus strains are foodborne pathogens responsible for two types of gastrointestinal diseases, diarrhea and emesis, caused by distinct toxins. Thus, the persistency of biofilms is of particular concern for the food industry, and understanding the underlying mechanisms of biofilm formation contributes to cleaning procedures. This review focuses on the genetic background underpinning the regulation of biofilm development, as well as the matrix components associated with biofilms. We also reflect on the correlation between biofilm formation and the development of highly resistant spores. Finally, advances in our understanding of the ecological importance and evolution of biofilm formation in the B. cereus group are discussed.
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27
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Lin Y, Alstrup M, Pang JKY, Maróti G, Er-Rafik M, Tourasse N, Økstad OA, Kovács ÁT. Adaptation of Bacillus thuringiensis to Plant Colonization Affects Differentiation and Toxicity. mSystems 2021; 6:e0086421. [PMID: 34636664 PMCID: PMC8510532 DOI: 10.1128/msystems.00864-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/27/2021] [Indexed: 01/11/2023] Open
Abstract
The Bacillus cereus group (Bacillus cereus sensu lato) has a diverse ecology, including various species that are vertebrate or invertebrate pathogens. Few isolates from the B. cereus group have however been demonstrated to benefit plant growth. Therefore, it is crucial to explore how bacterial development and pathogenesis evolve during plant colonization. Herein, we investigated Bacillus thuringiensis (Cry-) adaptation to the colonization of Arabidopsis thaliana roots and monitored changes in cellular differentiation in experimentally evolved isolates. Isolates from two populations displayed improved iterative ecesis on roots and increased virulence against insect larvae. Molecular dissection and recreation of a causative mutation revealed the importance of a nonsense mutation in the rho transcription terminator gene. Transcriptome analysis revealed how Rho impacts various B. thuringiensis genes involved in carbohydrate metabolism and virulence. Our work suggests that evolved multicellular aggregates have a fitness advantage over single cells when colonizing plants, creating a trade-off between swimming and multicellularity in evolved lineages, in addition to unrelated alterations in pathogenicity. IMPORTANCE Biologicals-based plant protection relies on the use of safe microbial strains. During application of biologicals to the rhizosphere, microbes adapt to the niche, including genetic mutations shaping the physiology of the cells. Here, the experimental evolution of Bacillus thuringiensis lacking the insecticide crystal toxins was examined on the plant root to reveal how adaptation shapes the differentiation of this bacterium. Interestingly, evolution of certain lineages led to increased hemolysis and insect larva pathogenesis in B. thuringiensis driven by transcriptional rewiring. Further, our detailed study reveals how inactivation of the transcription termination protein Rho promotes aggregation on the plant root in addition to altered differentiation and pathogenesis in B. thuringiensis.
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Affiliation(s)
- Yicen Lin
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Monica Alstrup
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Janet Ka Yan Pang
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Mériem Er-Rafik
- National Centre for Nano Fabrication and Characterization, Technical University of Denmark, Lyngby, Denmark
| | - Nicolas Tourasse
- Université Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, Bordeaux, France
| | - Ole Andreas Økstad
- Centre for Integrative Microbial Evolution, University of Oslo, Oslo, Norway
- Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Ákos T. Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark
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28
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Arnaouteli S, Bamford NC, Stanley-Wall NR, Kovács ÁT. Bacillus subtilis biofilm formation and social interactions. Nat Rev Microbiol 2021; 19:600-614. [PMID: 33824496 DOI: 10.1038/s41579-021-00540-9] [Citation(s) in RCA: 148] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2021] [Indexed: 02/03/2023]
Abstract
Biofilm formation is a process in which microbial cells aggregate to form collectives that are embedded in a self-produced extracellular matrix. Bacillus subtilis is a Gram-positive bacterium that is used to dissect the mechanisms controlling matrix production and the subsequent transition from a motile planktonic cell state to a sessile biofilm state. The collective nature of life in a biofilm allows emergent properties to manifest, and B. subtilis biofilms are linked with novel industrial uses as well as probiotic and biocontrol processes. In this Review, we outline the molecular details of the biofilm matrix and the regulatory pathways and external factors that control its production. We explore the beneficial outcomes associated with biofilms. Finally, we highlight major advances in our understanding of concepts of microbial evolution and community behaviour that have resulted from studies of the innate heterogeneity of biofilms.
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Affiliation(s)
- Sofia Arnaouteli
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Natalie C Bamford
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK.
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark.
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29
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Blake C, Nordgaard M, Maróti G, Kovács ÁT. Diversification of Bacillus subtilis during experimental evolution on Arabidopsis thaliana and the complementarity in root colonization of evolved subpopulations. Environ Microbiol 2021; 23:6122-6136. [PMID: 34296794 DOI: 10.1111/1462-2920.15680] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 12/17/2022]
Abstract
The soil bacterium Bacillus subtilis is known to suppress pathogens as well as promote plant growth. However, in order to fully exploit the potential as natural fertilizer, we need a better understanding of the interactions between B. subtilis and plants. Here, B. subtilis was examined for root colonization through experimental evolution on Arabidopsis thaliana. The populations evolved rapidly, improved in root colonization and diversified into three distinct morphotypes. In order to better understand the adaptation that had taken place, single evolved isolates from the final transfer were randomly selected for further characterization, revealing changes in growth and pellicle formation in medium supplemented with plant polysaccharides. Intriguingly, certain evolved isolates showed improved root colonization only on the plant species they evolved on, but not on another plant species, namely tomato, suggesting A. thaliana specific adaption paths. Finally, the mix performed better than the sum of its constituents in monoculture, which was demonstrated to be caused by complementarity effects. Our results suggest that genetic diversification occurs in an ecological relevant setting on plant roots and proves to be a stable strategy for root colonization.
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Affiliation(s)
- Christopher Blake
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Mathilde Nordgaard
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, 6726, Hungary
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
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30
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Dragoš A, Andersen AJC, Lozano-Andrade CN, Kempen PJ, Kovács ÁT, Strube ML. Phages carry interbacterial weapons encoded by biosynthetic gene clusters. Curr Biol 2021; 31:3479-3489.e5. [PMID: 34186025 DOI: 10.1016/j.cub.2021.05.046] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 04/16/2021] [Accepted: 05/20/2021] [Indexed: 01/08/2023]
Abstract
Bacteria produce diverse specialized metabolites that mediate ecological interactions and serve as a rich source of industrially relevant natural products. Biosynthetic pathways for these metabolites are encoded by organized groups of genes called biosynthetic gene clusters (BGCs). Understanding the natural function and distribution of BGCs provides insight into the mechanisms through which microorganisms interact and compete. Further, understanding BGCs is extremely important for biocontrol and the mining of new bioactivities. Here, we investigated phage-encoded BGCs (pBGCs), challenging the relationship between phage origin and BGC structure and function. The results demonstrated that pBGCs are rare, and they predominantly reside within temperate phages infecting commensal or pathogenic bacterial hosts. Further, the vast majority of pBGCs were found to encode for bacteriocins. Using the soil- and gut-associated bacterium Bacillus subtilis, we experimentally demonstrated how a temperate phage equips a bacterium with a fully functional BGC, providing a clear competitive fitness advantage over the ancestor. Moreover, we demonstrated a similar transfer of the same phage in prophage form. Finally, using genetic and genomic comparisons, a strong association between pBGC type and phage host range was revealed. These findings suggest that bacteriocins are encoded in temperate phages of a few commensal bacterial genera. In these cases, lysogenic conversion provides an evolutionary benefit to the infected host and, hence, to the phage itself. This study is an important step toward understanding the natural role of bacterial compounds encoded by BGCs, the mechanisms driving their horizontal transfer, and the sometimes mutualistic relationship between bacteria and temperate phages.
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Affiliation(s)
- Anna Dragoš
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark.
| | - Aaron J C Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark
| | - Carlos N Lozano-Andrade
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark
| | - Paul J Kempen
- Department of Health Technology, Technical University of Denmark, Produktionstorvet bldg. 423, DK-2800 Kgs Lyngby, Denmark; National Center for Nano Fabrication and Characterization, Technical University of Denmark, Fysikvej bldg. 307, DK-2800 Kgs Lyngby, Denmark
| | - Ákos T Kovács
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark.
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31
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Nordgaard M, Mortensen RMR, Kirk NK, Gallegos‐Monterrosa R, Kovács ÁT. Deletion of Rap-Phr systems in Bacillus subtilis influences in vitro biofilm formation and plant root colonization. Microbiologyopen 2021; 10:e1212. [PMID: 34180604 PMCID: PMC8236291 DOI: 10.1002/mbo3.1212] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 12/19/2022] Open
Abstract
Natural isolates of the soil-dwelling bacterium Bacillus subtilis form robust biofilms under laboratory conditions and colonize plant roots. B. subtilis biofilm gene expression displays phenotypic heterogeneity that is influenced by a family of Rap-Phr regulatory systems. Most Rap-Phr systems in B. subtilis have been studied independently, in different genetic backgrounds and under distinct conditions, hampering true comparison of the Rap-Phr systems' impact on bacterial cell differentiation. Here, we investigated each of the 12 Rap-Phr systems of B.subtilis NCIB 3610 for their effect on biofilm formation. By studying single ∆rap-phr mutants, we show that despite redundancy between the cell-cell communication systems, deletion of each of the 12 Rap-Phr systems influences matrix gene expression. These Rap-Phr systems therefore enable fine-tuning of the timing and level of matrix production in response to specific conditions. Furthermore, some of the ∆rap-phr mutants demonstrated altered biofilm formation in vitro and colonization of Arabidopsis thaliana roots, but not necessarily similarly in both processes, indicating that the pathways regulating matrix gene expression and other factors important for biofilm formation may be differently regulated under these distinct conditions.
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Affiliation(s)
- Mathilde Nordgaard
- Bacterial Interactions and Evolution GroupDTU BioengineeringTechnical University of DenmarkLyngbyDenmark
| | | | - Nikolaj Kaae Kirk
- Bacterial Interactions and Evolution GroupDTU BioengineeringTechnical University of DenmarkLyngbyDenmark
| | | | - Ákos T. Kovács
- Bacterial Interactions and Evolution GroupDTU BioengineeringTechnical University of DenmarkLyngbyDenmark
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32
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Gallegos-Monterrosa R, Christensen MN, Barchewitz T, Koppenhöfer S, Priyadarshini B, Bálint B, Maróti G, Kempen PJ, Dragoš A, Kovács ÁT. Impact of Rap-Phr system abundance on adaptation of Bacillus subtilis. Commun Biol 2021; 4:468. [PMID: 33850233 PMCID: PMC8044106 DOI: 10.1038/s42003-021-01983-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/12/2021] [Indexed: 02/07/2023] Open
Abstract
Microbes commonly display great genetic plasticity, which has allowed them to colonize all ecological niches on Earth. Bacillus subtilis is a soil-dwelling organism that can be isolated from a wide variety of environments. An interesting characteristic of this bacterium is its ability to form biofilms that display complex heterogeneity: individual, clonal cells develop diverse phenotypes in response to different environmental conditions within the biofilm. Here, we scrutinized the impact that the number and variety of the Rap-Phr family of regulators and cell-cell communication modules of B. subtilis has on genetic adaptation and evolution. We examine how the Rap family of phosphatase regulators impacts sporulation in diverse niches using a library of single and double rap-phr mutants in competition under 4 distinct growth conditions. Using specific DNA barcodes and whole-genome sequencing, population dynamics were followed, revealing the impact of individual Rap phosphatases and arising mutations on the adaptability of B. subtilis.
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Affiliation(s)
- Ramses Gallegos-Monterrosa
- grid.9613.d0000 0001 1939 2794Terrestrial Biofilms Group, Institute of Microbiology, Friedrich-Schiller-University Jena, Jena, Germany
| | - Mathilde Nordgaard Christensen
- grid.5170.30000 0001 2181 8870Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tino Barchewitz
- grid.9613.d0000 0001 1939 2794Terrestrial Biofilms Group, Institute of Microbiology, Friedrich-Schiller-University Jena, Jena, Germany
| | - Sonja Koppenhöfer
- grid.9613.d0000 0001 1939 2794Terrestrial Biofilms Group, Institute of Microbiology, Friedrich-Schiller-University Jena, Jena, Germany ,grid.25055.370000 0000 9130 6822Present Address: Department of Biology, Memorial University of Newfoundland, St. John’s, NL Canada
| | - B. Priyadarshini
- grid.5170.30000 0001 2181 8870Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Balázs Bálint
- grid.475919.7Seqomics Biotechnology Ltd., Mórahalom, Hungary
| | - Gergely Maróti
- grid.5018.c0000 0001 2149 4407Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Paul J. Kempen
- grid.5170.30000 0001 2181 8870Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anna Dragoš
- grid.5170.30000 0001 2181 8870Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ákos T. Kovács
- grid.9613.d0000 0001 1939 2794Terrestrial Biofilms Group, Institute of Microbiology, Friedrich-Schiller-University Jena, Jena, Germany ,grid.5170.30000 0001 2181 8870Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
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33
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Steinke K, Mohite OS, Weber T, Kovács ÁT. Phylogenetic Distribution of Secondary Metabolites in the Bacillus subtilis Species Complex. mSystems 2021; 6:e00057-21. [PMID: 33688015 PMCID: PMC8546965 DOI: 10.1128/msystems.00057-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 02/19/2021] [Indexed: 12/20/2022] Open
Abstract
Microbes produce a plethora of secondary (or specialized) metabolites that, although not essential for primary metabolism, benefit them to survive in the environment, communicate, and influence cell differentiation. Biosynthetic gene clusters (BGCs), responsible for the production of these secondary metabolites, are readily identifiable on bacterial genome sequences. Understanding the phylogeny and distribution of BGCs helps us to predict the natural product synthesis ability of new isolates. Here, we examined 310 genomes from the Bacillus subtilis group, determined the inter- and intraspecies patterns of absence/presence for all BGCs, and assigned them to defined gene cluster families (GCFs). This allowed us to establish patterns in the distribution of both known and unknown products. Further, we analyzed variations in the BGC structures of particular families encoding natural products, such as plipastatin, fengycin, iturin, mycosubtilin, and bacillomycin. Our detailed analysis revealed multiple GCFs that are species or clade specific and a few others that are scattered within or between species, which will guide exploration of the chemodiversity within the B. subtilis group. Surprisingly, we discovered that partial deletion of BGCs and frameshift mutations in selected biosynthetic genes are conserved within phylogenetically related isolates, although isolated from around the globe. Our results highlight the importance of detailed genomic analysis of BGCs and the remarkable phylogenetically conserved erosion of secondary metabolite biosynthetic potential in the B. subtilis group.IMPORTANCE Members of the B. subtilis species complex are commonly recognized producers of secondary metabolites, among those, the production of antifungals, which makes them promising biocontrol strains. While there are studies examining the distribution of well-known secondary metabolites in Bacilli, intraspecies clade-specific distribution has not been systematically reported for the B. subtilis group. Here, we report the complete biosynthetic potential within the B. subtilis group to explore the distribution of the biosynthetic gene clusters and to reveal an exhaustive phylogenetic conservation of secondary metabolite production within Bacillus that supports the chemodiversity within this species complex. We identify that certain gene clusters acquired deletions of genes and particular frameshift mutations, rendering them inactive for secondary metabolite biosynthesis, a conserved genetic trait within phylogenetically conserved clades of certain species. The overview guides the assignment of the secondary metabolite production potential of newly isolated Bacillus strains based on genome sequence and phylogenetic relatedness.
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Affiliation(s)
- Kat Steinke
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Omkar S Mohite
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
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34
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Hartmann R, Jeckel H, Jelli E, Singh PK, Vaidya S, Bayer M, Rode DKH, Vidakovic L, Díaz-Pascual F, Fong JCN, Dragoš A, Lamprecht O, Thöming JG, Netter N, Häussler S, Nadell CD, Sourjik V, Kovács ÁT, Yildiz FH, Drescher K. Publisher Correction: Quantitative image analysis of microbial communities with BiofilmQ. Nat Microbiol 2021; 6:270. [PMID: 33420476 PMCID: PMC7840498 DOI: 10.1038/s41564-021-00863-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Raimo Hartmann
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Hannah Jeckel
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Eric Jelli
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Praveen K Singh
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sanika Vaidya
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Miriam Bayer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Daniel K H Rode
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Lucia Vidakovic
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Jiunn C N Fong
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, USA
| | - Anna Dragoš
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Olga Lamprecht
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dubendorf, Switzerland
| | - Janne G Thöming
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany.,Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Niklas Netter
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany.,Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Carey D Nadell
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Zentrum für Synthetische Mikrobiologie, SYNMIKRO, Marburg, Germany
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, USA
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany. .,Department of Physics, Philipps-Universität Marburg, Marburg, Germany. .,Zentrum für Synthetische Mikrobiologie, SYNMIKRO, Marburg, Germany.
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35
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Eelderink-Chen Z, Bosman J, Sartor F, Dodd AN, Kovács ÁT, Merrow M. A circadian clock in a nonphotosynthetic prokaryote. Sci Adv 2021; 7:eabe2086. [PMID: 33523996 PMCID: PMC7793578 DOI: 10.1126/sciadv.abe2086] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/13/2020] [Indexed: 05/06/2023]
Abstract
Circadian clocks create a 24-hour temporal structure, which allows organisms to occupy a niche formed by time rather than space. They are pervasive throughout nature, yet they remain unexpectedly unexplored and uncharacterized in nonphotosynthetic bacteria. Here, we identify in Bacillus subtilis circadian rhythms sharing the canonical properties of circadian clocks: free-running period, entrainment, and temperature compensation. We show that gene expression in B. subtilis can be synchronized in 24-hour light or temperature cycles and exhibit phase-specific characteristics of entrainment. Upon release to constant dark and temperature conditions, bacterial biofilm populations have temperature-compensated free-running oscillations with a period close to 24 hours. Our work opens the field of circadian clocks in the free-living, nonphotosynthetic prokaryotes, bringing considerable potential for impact upon biomedicine, ecology, and industrial processes.
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Affiliation(s)
- Zheng Eelderink-Chen
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Goethestrasse 31, 80336 Munich, Germany
| | - Jasper Bosman
- Department of Bioinformatics, Hanze University of Applied Sciences, Groningen, Zernikeplein 11, 9747 AS Groningen, Netherlands
| | - Francesca Sartor
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Goethestrasse 31, 80336 Munich, Germany
| | - Antony N Dodd
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Martha Merrow
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Goethestrasse 31, 80336 Munich, Germany.
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36
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Abstract
Bacillus subtilis is one of the most widely studied plant growth-promoting rhizobacteria. It is able to promote plant growth as well as control plant pathogens through diverse mechanisms, including the improvement of nutrient availability and alteration of phytohormone homeostasis as well as the production of antimicrobials and triggering induced systemic resistance, respectively. Even though its benefits for crop production have been recognized and studied extensively under laboratory conditions, the success of its application in fields varies immensely. It is widely accepted that agricultural application of B. subtilis often fails because the bacteria are not able to persist in the rhizosphere. Bacterial colonization of plant roots is a crucial step in the interaction between microbe and plant and seems, therefore, to be of great importance for its growth promotion and biocontrol effects. A successful root colonization depends thereby on both bacterial traits, motility and biofilm formation, as well as on a signal interplay with the plant. This review addresses current knowledge about plant-microbial interactions of the B. subtilis species, including the various mechanisms for supporting plant growth as well as the necessity for the establishment of the relationship.[Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.
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Affiliation(s)
- Christopher Blake
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark
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37
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Dragoš A, Priyadarshini B, Hasan Z, Strube ML, Kempen PJ, Maróti G, Kaspar C, Bose B, Burton BM, Bischofs IB, Kovács ÁT. Pervasive prophage recombination occurs during evolution of spore-forming Bacilli. ISME J 2020; 15:1344-1358. [PMID: 33343000 DOI: 10.1038/s41396-020-00854-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/12/2020] [Accepted: 11/20/2020] [Indexed: 02/06/2023]
Abstract
Phages are the main source of within-species bacterial diversity and drivers of horizontal gene transfer, but we know little about the mechanisms that drive genetic diversity of these mobile genetic elements (MGEs). Recently, we showed that a sporulation selection regime promotes evolutionary changes within SPβ prophage of Bacillus subtilis, leading to direct antagonistic interactions within the population. Herein, we reveal that under a sporulation selection regime, SPβ recombines with low copy number phi3Ts phage DNA present within the B. subtilis population. Recombination results in a new prophage occupying a different integration site, as well as the spontaneous release of virulent phage hybrids. Analysis of Bacillus sp. strains suggests that SPβ and phi3T belong to a distinct cluster of unusually large phages inserted into sporulation-related genes that are equipped with a spore-related genetic arsenal. Comparison of Bacillus sp. genomes indicates that similar diversification of SPβ-like phages takes place in nature. Our work is a stepping stone toward empirical studies on phage evolution, and understanding the eco-evolutionary relationships between bacteria and their phages. By capturing the first steps of new phage evolution, we reveal striking relationship between survival strategy of bacteria and evolution of their phages.
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Affiliation(s)
- Anna Dragoš
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
| | - B Priyadarshini
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Zahraa Hasan
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Mikael Lenz Strube
- Bacterial Ecophysiology and Biotechnology Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Paul J Kempen
- Department of Health Technology, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, H-6701, Hungary
| | - Charlotte Kaspar
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | | | - Briana M Burton
- Department of Bacteriology, University of Wisconsin, Madison, WI, 53706, USA
| | - Ilka B Bischofs
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
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38
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Kiesewalter HT, Lozano-Andrade CN, Strube ML, Kovács ÁT. Secondary metabolites of Bacillus subtilis impact the assembly of soil-derived semisynthetic bacterial communities. Beilstein J Org Chem 2020; 16:2983-2998. [PMID: 33335606 PMCID: PMC7722629 DOI: 10.3762/bjoc.16.248] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/18/2020] [Indexed: 12/26/2022] Open
Abstract
Secondary metabolites provide Bacillus subtilis with increased competitiveness towards other microorganisms. In particular, nonribosomal peptides (NRPs) have an enormous antimicrobial potential by causing cell lysis, perforation of fungal membranes, enzyme inhibition, or disruption of bacterial protein synthesis. This knowledge was primarily acquired in vitro when B. subtilis was competing with other microbial monocultures. However, our understanding of the true ecological role of these small molecules is limited. In this study, we have established soil-derived semisynthetic mock communities containing 13 main genera and supplemented them with B. subtilis P5_B1 WT, the NRP-deficient strain sfp, or single-NRP mutants incapable of producing surfactin, plipastatin, or bacillaene. Through 16S amplicon sequencing, it was revealed that the invasion of NRP-producing B. subtilis strains had no major impact on the bacterial communities. Still, the abundance of the two genera Lysinibacillus and Viridibacillus was reduced. Interestingly, this effect was diminished in communities supplemented with the NRP-deficient strain. Growth profiling of Lysinibacillus fusiformis M5 exposed to either spent media of the B. subtilis strains or pure surfactin indicated the sensitivity of this strain towards the biosurfactant surfactin. Our study provides a more in-depth insight into the influence of B. subtilis NRPs on semisynthetic bacterial communities and helps to understand their ecological role.
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Affiliation(s)
- Heiko T Kiesewalter
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Carlos N Lozano-Andrade
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Mikael L Strube
- Bacterial Ecophysiology and Biotechnology Group, DTU Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs. Lyngby, Denmark
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39
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Garde R, Ewald J, Kovács ÁT, Schuster S. Modelling population dynamics in a unicellular social organism community using a minimal model and evolutionary game theory. Open Biol 2020; 10:200206. [PMID: 33142084 PMCID: PMC7729035 DOI: 10.1098/rsob.200206] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Most unicellular organisms live in communities and express different phenotypes. Many efforts have been made to study the population dynamics of such complex communities of cells, coexisting as well-coordinated units. Minimal models based on ordinary differential equations are powerful tools that can help us understand complex phenomena. They represent an appropriate compromise between complexity and tractability; they allow a profound and comprehensive analysis, which is still easy to understand. Evolutionary game theory is another powerful tool that can help us understand the costs and benefits of the decision a particular cell of a unicellular social organism takes when faced with the challenges of the biotic and abiotic environment. This work is a binocular view at the population dynamics of such a community through the objectives of minimal modelling and evolutionary game theory. We test the behaviour of the community of a unicellular social organism at three levels of antibiotic stress. Even in the absence of the antibiotic, spikes in the fraction of resistant cells can be observed indicating the importance of bet hedging. At moderate level of antibiotic stress, we witness cyclic dynamics reminiscent of the renowned rock–paper–scissors game. At a very high level, the resistant type of strategy is the most favourable.
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Affiliation(s)
- Ravindra Garde
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany.,Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745 Jena, Germany
| | - Jan Ewald
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Søltofts Plads Building 221, 2800 Kongens Lyngby, Denmark
| | - Stefan Schuster
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
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40
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Abstract
Assembly of microbial communities is shaped by various physical and chemical factors deriving from their environment, including other microbes inhabiting the certain niche. In addition to direct cell-cell contacts, primary and secondary metabolites impact the growth of microbial community members. Metabolites might act as growth-promoting (e.g., cross-feeding), growth-inhibiting (e.g., antimicrobials) or signalling molecules. In multi-species microbial assemblies, secreted metabolites might influence specific members of the community, altering species abundances and therefore the functioning of these microcosms. In the current issue, Cosetta and colleagues describe a unique volatile metabolite-mediated cross-kingdom interaction that shapes the cheese rind community assembly. The study paves the way of our understanding how fungus-produced volatile compounds promote the growth of a certain bacterial genus, a principal connection between community members of the cheese rind.
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Affiliation(s)
- Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
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41
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Otto SB, Martin M, Schäfer D, Hartmann R, Drescher K, Brix S, Dragoš A, Kovács ÁT. Privatization of Biofilm Matrix in Structurally Heterogeneous Biofilms. mSystems 2020; 5:e00425-20. [PMID: 32753507 PMCID: PMC7406226 DOI: 10.1128/msystems.00425-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/13/2020] [Indexed: 12/19/2022] Open
Abstract
The self-produced biofilm provides beneficial protection for the enclosed cells, but the costly production of matrix components makes producer cells susceptible to cheating by nonproducing individuals. Despite detrimental effects of nonproducers, biofilms can be heterogeneous, with isogenic nonproducers being a natural consequence of phenotypic differentiation processes. For instance, in Bacillus subtilis biofilm cells differ in production of the two major matrix components, the amyloid fiber protein TasA and exopolysaccharides (EPS), demonstrating different expression levels of corresponding matrix genes. This raises questions regarding matrix gene expression dynamics during biofilm development and the impact of phenotypic nonproducers on biofilm robustness. Here, we show that biofilms are structurally heterogeneous and can be separated into strongly and weakly associated clusters. We reveal that spatiotemporal changes in structural heterogeneity correlate with matrix gene expression, with TasA playing a key role in biofilm integrity and timing of development. We show that the matrix remains partially privatized by the producer subpopulation, where cells tightly stick together even when exposed to shear stress. Our results support previous findings on the existence of "weak points" in seemingly robust biofilms as well as on the key role of linkage proteins in biofilm formation. Furthermore, we provide a starting point for investigating the privatization of common goods within isogenic populations.IMPORTANCE Biofilms are communities of bacteria protected by a self-produced extracellular matrix. The detrimental effects of nonproducing individuals on biofilm development raise questions about the dynamics between community members, especially when isogenic nonproducers exist within wild-type populations. We asked ourselves whether phenotypic nonproducers impact biofilm robustness, and where and when this heterogeneity of matrix gene expression occurs. Based on our results, we propose that the matrix remains partly privatized by the producing subpopulation, since producing cells stick together when exposed to shear stress. The important role of linkage proteins in robustness and development of the structurally heterogeneous biofilm provides an entry into studying the privatization of common goods within isogenic populations.
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Affiliation(s)
- Simon B Otto
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Marivic Martin
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Daniel Schäfer
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Raimo Hartmann
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Susanne Brix
- Disease Systems Immunology Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anna Dragoš
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
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42
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Martin M, Dragoš A, Otto SB, Schäfer D, Brix S, Maróti G, Kovács ÁT. Cheaters shape the evolution of phenotypic heterogeneity in Bacillus subtilis biofilms. ISME J 2020; 14:2302-2312. [PMID: 32483306 PMCID: PMC7608354 DOI: 10.1038/s41396-020-0685-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/06/2020] [Accepted: 05/13/2020] [Indexed: 01/18/2023]
Abstract
Biofilms are closely packed cells held and shielded by extracellular matrix composed of structural proteins and exopolysaccharides (EPS). As matrix components are costly to produce and shared within the population, EPS-deficient cells can act as cheaters by gaining benefits from the cooperative nature of EPS producers. Remarkably, genetically programmed EPS producers can also exhibit phenotypic heterogeneity at single-cell level. Previous studies have shown that spatial structure of biofilms limits the spread of cheaters, but the long-term influence of cheating on biofilm evolution is not well understood. Here, we examine the influence of EPS nonproducers on evolution of matrix production within the populations of EPS producers in a model biofilm-forming bacterium, Bacillus subtilis. We discovered that general adaptation to biofilm lifestyle leads to an increase in phenotypical heterogeneity of eps expression. However, prolonged exposure to EPS-deficient cheaters may result in different adaptive strategy, where eps expression increases uniformly within the population. We propose a molecular mechanism behind such adaptive strategy and demonstrate how it can benefit the EPS producers in the presence of cheaters. This study provides additional insights on how biofilms adapt and respond to stress caused by exploitation in long-term scenario.
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Affiliation(s)
- Marivic Martin
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.,Terrestrial Biofilms Group, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Anna Dragoš
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Simon B Otto
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Daniel Schäfer
- Terrestrial Biofilms Group, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Susanne Brix
- Disease Systems Immunology Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center of the Hungarian Academy of Sciences, Szeged, 6726, Hungary
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark. .,Terrestrial Biofilms Group, Friedrich Schiller University Jena, 07743, Jena, Germany.
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43
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Thérien M, Kiesewalter HT, Auria E, Charron-Lamoureux V, Wibowo M, Maróti G, Kovács ÁT, Beauregard PB. Surfactin production is not essential for pellicle and root-associated biofilm development of Bacillus subtilis. Biofilm 2020; 2:100021. [PMID: 33447807 PMCID: PMC7798449 DOI: 10.1016/j.bioflm.2020.100021] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/11/2020] [Accepted: 02/17/2020] [Indexed: 02/06/2023] Open
Abstract
Secondary metabolites have an important impact on the biocontrol potential of soil-derived microbes. In addition, various microbe-produced chemicals have been suggested to impact the development and phenotypic differentiation of bacteria, including biofilms. The non-ribosomal synthesized lipopeptide of Bacillus subtilis, surfactin, has been described to impact the plant promoting capacity of the bacterium. Here, we investigated the impact of surfactin production on biofilm formation of B. subtilis using the laboratory model systems; pellicle formation at the air-medium interface and architecturally complex colony development, in addition to plant root-associated biofilms. We found that the production of surfactin by B. subtilis is not essential for pellicle biofilm formation neither in the well-studied strain, NCIB 3610, nor in the newly isolated environmental strains, but lack of surfactin reduces colony expansion. Further, plant root colonization was comparable both in the presence or absence of surfactin synthesis. Our results suggest that surfactin-related biocontrol and plant promotion in B. subtilis strains are independent of biofilm formation.
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Affiliation(s)
- Maude Thérien
- Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Heiko T Kiesewalter
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Emile Auria
- Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada.,Biology Department, Ecole Normale Supérieure Paris-Saclay, Paris-Saclay University, Cachan, France
| | - Vincent Charron-Lamoureux
- Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Mario Wibowo
- Natural Product Discovery Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Pascale B Beauregard
- Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada
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44
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Garde R, Ibrahim B, Kovács ÁT, Schuster S. Differential equation-based minimal model describing metabolic oscillations in Bacillus subtilis biofilms. R Soc Open Sci 2020; 7:190810. [PMID: 32257302 PMCID: PMC7062081 DOI: 10.1098/rsos.190810] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 01/15/2020] [Indexed: 06/11/2023]
Abstract
Biofilms offer an excellent example of ecological interaction among bacteria. Temporal and spatial oscillations in biofilms are an emerging topic. In this paper, we describe the metabolic oscillations in Bacillus subtilis biofilms by applying the smallest theoretical chemical reaction system showing Hopf bifurcation proposed by Wilhelm and Heinrich in 1995. The system involves three differential equations and a single bilinear term. We specifically select parameters that are suitable for the biological scenario of biofilm oscillations. We perform computer simulations and a detailed analysis of the system including bifurcation analysis and quasi-steady-state approximation. We also discuss the feedback structure of the system and the correspondence of the simulations to biological observations. Our theoretical work suggests potential scenarios about the oscillatory behaviour of biofilms and also serves as an application of a previously described chemical oscillator to a biological system.
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Affiliation(s)
- Ravindra Garde
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745 Jena, Germany
| | - Bashar Ibrahim
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
- Centre for Applied Mathematics and Bioinformatics, Gulf University for Science and Technology, Hawally 32093, Kuwait
- Department of Mathematics and Natural Sciences, Gulf University for Science and Technology, Hawally 32093, Kuwait
| | - Ákos T. Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Søltofts Plads Building 221, 2800 Kgs. Lyngby, Denmark
| | - Stefan Schuster
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
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45
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Kiesewalter HT, Lozano-Andrade CN, Maróti G, Snyder D, Cooper VS, Jørgensen TS, Weber T, Kovács ÁT. Complete Genome Sequences of 13 Bacillus subtilis Soil Isolates for Studying Secondary Metabolite Diversity. Microbiol Resour Announc 2020; 9:e01406-19. [PMID: 31919181 PMCID: PMC6952667 DOI: 10.1128/mra.01406-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 12/10/2019] [Indexed: 02/07/2023] Open
Abstract
Bacillus subtilis is a plant-benefiting soil-dwelling Gram-positive bacterium with secondary metabolite production potential. Here, we report the complete genome sequences of 13 B. subtilis strains isolated from different soil samples in Germany and Denmark.
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Affiliation(s)
- Heiko T Kiesewalter
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Carlos N Lozano-Andrade
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Dan Snyder
- Microbial Genome Sequencing Center, Pittsburgh, Pennsylvania, USA
| | - Vaughn S Cooper
- Microbial Genome Sequencing Center, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Tue Sparholt Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
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46
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Falcón García C, Kretschmer M, Lozano-Andrade CN, Schönleitner M, Dragoŝ A, Kovács ÁT, Lieleg O. Metal ions weaken the hydrophobicity and antibiotic resistance of Bacillus subtilis NCIB 3610 biofilms. NPJ Biofilms Microbiomes 2020; 6:1. [PMID: 31908831 PMCID: PMC6941983 DOI: 10.1038/s41522-019-0111-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 12/03/2019] [Indexed: 02/06/2023] Open
Abstract
Surface superhydrophobicity makes bacterial biofilms very difficult to fight, and it is a combination of their matrix composition and complex surface roughness which synergistically protects these biomaterials from wetting. Although trying to eradicate biofilms with aqueous (antibiotic) solutions is common practice, this can be a futile approach if the biofilms have superhydrophobic properties. To date, there are not many options available to reduce the liquid repellency of biofilms or to prevent this material property from developing. Here, we present a solution to this challenge. We demonstrate how the addition of metal ions such as copper and zinc during or after biofilm formation can render the surface of otherwise superhydrophobic B. subtilis NCIB 3610 biofilms completely wettable. As a result of this procedure, these smoother, hydrophilic biofilms are more susceptible to aqueous antibiotics solutions. Our strategy proposes a scalable and widely applicable step in a multi-faceted approach to eradicate biofilms.
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Affiliation(s)
- Carolina Falcón García
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Martin Kretschmer
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Carlos N. Lozano-Andrade
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800 Kongens Lyngby, Denmark
| | - Markus Schönleitner
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Anna Dragoŝ
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800 Kongens Lyngby, Denmark
| | - Ákos T. Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800 Kongens Lyngby, Denmark
| | - Oliver Lieleg
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
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47
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Kjeldgaard B, Listian SA, Ramaswamhi V, Richter A, Kiesewalter HT, Kovács ÁT. Fungal hyphae colonization by Bacillus subtilis relies on biofilm matrix components. Biofilm 2019; 1:100007. [PMID: 33447794 PMCID: PMC7798453 DOI: 10.1016/j.bioflm.2019.100007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/15/2019] [Accepted: 10/19/2019] [Indexed: 02/07/2023] Open
Abstract
Bacteria interact with their environment including microbes and higher eukaryotes. The ability of bacteria and fungi to affect each other are defined by various chemical, physical and biological factors. During physical association, bacterial cells can directly attach and settle on the hyphae of various fungal species. Such colonization of mycelia was proposed to be dependent on biofilm formation by the bacteria, but the essentiality of the biofilm matrix was not represented before. Here, we demonstrate that secreted biofilm matrix components of the soil-dwelling bacterium, Bacillus subtilis are essential for the establishment of a dense bacterial population on the hyphae of the filamentous black mold fungus, Aspergillus niger and the basidiomycete mushroom, Agaricus bisporus. We further illustrate that these matrix components can be shared among various mutants highlighting the community shaping impact of biofilm formers on bacteria-fungi interactions.
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Affiliation(s)
- Bodil Kjeldgaard
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Stevanus A Listian
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Valliyammai Ramaswamhi
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Anne Richter
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Heiko T Kiesewalter
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
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48
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Devi S, Kiesewalter HT, Kovács R, Frisvad JC, Weber T, Larsen TO, Kovács ÁT, Ding L. Depiction of secondary metabolites and antifungal activity of Bacillus velezensis DTU001. Synth Syst Biotechnol 2019; 4:142-149. [PMID: 31508511 PMCID: PMC6719288 DOI: 10.1016/j.synbio.2019.08.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 12/25/2022] Open
Abstract
For a safe and sustainable environment, effective microbes as biocontrol agents are in high demand. We have isolated a new Bacillus velezensis strain DTU001, investigated its antifungal spectrum, sequenced its genome, and uncovered the production of lipopeptides in HPLC-HRMS analysis. To test the antifungal efficacy, extracts of B. velezensis DTU001 was tested against a range of twenty human or plant pathogenic fungi. We demonstrate that inhibitory potential of B. velezensis DTU001 against selected fungi is superior in comparison to single lipopeptide, either iturin or fengycin. The isolate showed analogous biofilm formation to other closely related Bacilli. To further support the biocontrol properties of the isolate, coculture with Candida albicans demonstrated that B. velezensis DTU001 exhibited excellent antiproliferation effect against C. albicans. In summary, the described isolate is a potential antifungal agent with a broad antifungal spectrum that might assist our aims to avoid hazardous pathogenic fungi and provide alternative to toxicity caused by chemicals.
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Affiliation(s)
- Sagarika Devi
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Heiko T Kiesewalter
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Renátó Kovács
- Department of Medical Microbiology, Faculty of Medicine, University of Debrecen, 4032, Debrecen, Hungary
| | - Jens Christian Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Tilmann Weber
- Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Thomas Ostenfeld Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Ákos T Kovács
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Ling Ding
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
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López-Goñi I, Giner-Lamia J, Álvarez-Ordoñez A, Benitez-Páez A, Claessen D, Cortesao M, de Toro M, García-Ruano D, Granato ET, Kovács ÁT, Romalde JL, Sana TG, Sánchez-Angulo M, Sangari FJ, Smits WK, Sturm T, Thomassin JL, Valdehuesa KNG, Zapotoczna M. #EUROmicroMOOC: using Twitter to share trends in Microbiology worldwide. FEMS Microbiol Lett 2019; 366:5521206. [DOI: 10.1093/femsle/fnz141] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 06/19/2019] [Indexed: 11/12/2022] Open
Abstract
ABSTRACT
Twitter is one of the most popular social media networks that, in recent years, has been increasingly used by researchers as a platform to share science and discuss ongoing work. Despite its popularity, Twitter is not commonly used as a medium to teach science. Here, we summarize the results of #EUROmicroMOOC: the first worldwide Microbiology Massive Open Online Course taught in English using Twitter. Content analytics indicated that more than 3 million users saw posts with the hashtag #EUROmicroMOOC, which resulted in over 42 million Twitter impressions worldwide. These analyses demonstrate that free Microbiology MOOCs shared on Twitter are valuable educational tools that reach broad audiences throughout the world. We also describe our experience teaching an entire Microbiology course using Twitter and provide recommendations when using social media to communicate science to a broad audience.
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Affiliation(s)
- I López-Goñi
- Departamento de Microbiología y Parasitología, Universidad de Navarra, E-31080 Pamplona, Spain
| | - J Giner-Lamia
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Campus Montegancedo-UPM, E-28223 Pozuelo de Alarcón, Madrid,Spain
- Departamento de Biotecnología-Biología Vegetal, ETSIAAB, UPM, Ciudad Universitaria, E-28040 Madrid, Spain
| | - A Álvarez-Ordoñez
- Departamento de Higiene y Tecnología de los Alimentos, Instituto de Ciencia y Tecnología de los Alimentos, Universidad de León, E-24071 León, Spain
| | - Alfonso Benitez-Páez
- Institute of Agrochemistry and Food Technology IATA-CSIC. C/Catedràtic Agustín Escardino Benlloch, 7, E-46980 Paterna-Valencia, Spain
| | - D Claessen
- Intitute of Biology, Leiden University, NL-2333 Leiden, the Netherlands
| | - M Cortesao
- German Aerospace Center (DLR), D-51147 Cologne, Germany
| | - M de Toro
- Fundacion Rioja Salud, E-26006 Logroño, Spain
| | - D García-Ruano
- Institute of Functional Biology and Genomics, USAL–CSIC, University of Salamanca, E-37002 Salamanca, Spain
| | - E T Granato
- Department of Zoology, University of Oxford, OX1 3SZ Oxford, United Kingdom
| | - Á T Kovács
- DTU Bioengineering, Bacterial Interactions and Evolution group,1 Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - J L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
| | - T G Sana
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - M Sánchez-Angulo
- Departamento de Producción Vegetal y Microbiología, University of Miguel Hernández, E-03202 Elche, Spain
| | - F J Sangari
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC) CSIC-University of Cantabria and Department of Molecular Biology, University of Cantabria, E-39011 Santander, Spain
| | - W K Smits
- Department of Medical Microbiology, Leiden University Medical Center, NL-2300 RC Leiden, the Netherlands
| | - T Sturm
- Cabrillo College, Aptos, CA 95003, USA
| | - J L Thomassin
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, 28 rue du Dr. Roux, Paris F-75724 France
| | - K N G Valdehuesa
- Department of Energy Science and Technology, Myongji University, 03674 South Korea
| | - M Zapotoczna
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
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Sartor F, Eelderink-Chen Z, Aronson B, Bosman J, Hibbert LE, Dodd AN, Kovács ÁT, Merrow M. Are There Circadian Clocks in Non-Photosynthetic Bacteria? Biology (Basel) 2019; 8:E41. [PMID: 31121908 PMCID: PMC6627678 DOI: 10.3390/biology8020041] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/15/2019] [Accepted: 05/15/2019] [Indexed: 01/01/2023]
Abstract
Circadian clocks in plants, animals, fungi, and in photosynthetic bacteria have been well-described. Observations of circadian rhythms in non-photosynthetic Eubacteria have been sporadic, and the molecular basis for these potential rhythms remains unclear. Here, we present the published experimental and bioinformatical evidence for circadian rhythms in these non-photosynthetic Eubacteria. From this, we suggest that the timekeeping functions of these organisms will be best observed and studied in their appropriate complex environments. Given the rich temporal changes that exist in these environments, it is proposed that microorganisms both adapt to and contribute to these daily dynamics through the process of temporal mutualism. Understanding the timekeeping and temporal interactions within these systems will enable a deeper understanding of circadian clocks and temporal programs and provide valuable insights for medicine and agriculture.
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Affiliation(s)
- Francesca Sartor
- Institute of Medical Psychology, Medical Faculty, LMU Munich, 80336 Munich, Germany.
| | - Zheng Eelderink-Chen
- Institute of Medical Psychology, Medical Faculty, LMU Munich, 80336 Munich, Germany.
| | - Ben Aronson
- Department of Biology, University of Redlands, Redlands, CA 92373, USA.
| | - Jasper Bosman
- Bioinformatics, Hanzehogeschool Groningen, 9747 AS Groningen, The Netherlands.
| | - Lauren E Hibbert
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK.
| | - Antony N Dodd
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK.
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
| | - Martha Merrow
- Institute of Medical Psychology, Medical Faculty, LMU Munich, 80336 Munich, Germany.
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