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Yang D, Zheng X, Jiang L, Ye M, He X, Jin Y, Wu R. Functional Mapping of Phenotypic Plasticity of Staphylococcus aureus Under Vancomycin Pressure. Front Microbiol 2021; 12:696730. [PMID: 34566908 PMCID: PMC8458881 DOI: 10.3389/fmicb.2021.696730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022] Open
Abstract
Phenotypic plasticity is the exhibition of various phenotypic traits produced by a single genotype in response to environmental changes, enabling organisms to adapt to environmental changes by maintaining growth and reproduction. Despite its significance in evolutionary studies, we still know little about the genetic control of phenotypic plasticity. In this study, we designed and conducted a genome-wide association study (GWAS) to reveal genetic architecture of how Staphylococcus aureus strains respond to increasing concentrations of vancomycin (0, 2, 4, and 6 μg/mL) in a time course. We implemented functional mapping, a dynamic model for genetic mapping using longitudinal data, to map specific loci that mediate the growth trajectories of abundance of vancomycin-exposed S. aureus strains. 78 significant single nucleotide polymorphisms were identified following analysis of the whole growth and development process, and seven genes might play a pivotal role in governing phenotypic plasticity to the pressure of vancomycin. These seven genes, SAOUHSC_00020 (walR), SAOUHSC_00176, SAOUHSC_00544 (sdrC), SAOUHSC_02998, SAOUHSC_00025, SAOUHSC_00169, and SAOUHSC_02023, were found to help S. aureus regulate antibiotic pressure. Our dynamic gene mapping technique provides a tool for dissecting the phenotypic plasticity mechanisms of S. aureus under vancomycin pressure, emphasizing the feasibility and potential of functional mapping in the study of bacterial phenotypic plasticity.
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Affiliation(s)
- Dengcheng Yang
- Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xuyang Zheng
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Libo Jiang
- Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Meixia Ye
- Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xiaoqing He
- Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yi Jin
- Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.,Department of Public Health Sciences and Statistics, Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, United States
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van Westreenen A, Zhang N, Douma JC, Evers JB, Anten NPR, Marcelis LFM. Substantial differences occur between canopy and ambient climate: Quantification of interactions in a greenhouse-canopy system. PLoS One 2020; 15:e0233210. [PMID: 32469897 PMCID: PMC7259515 DOI: 10.1371/journal.pone.0233210] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 04/14/2020] [Indexed: 11/18/2022] Open
Abstract
Organ temperature and variation therein plays a key role in plant functioning and its responses to e.g. climate change. There is a strong feedback between organ, especially leaf, temperature and the climate within the canopy (canopy climate), which in turn interacts with the climate outside the canopy (ambient climate). For greenhouses, the determinants of this interplay and how they drive differences between canopy and ambient climate are poorly understood. Yet, as many experiments on both regular greenhouse crops and field crops are done in greenhouses, this is crucial to know. Therefore, we designed an experiment to quantify the differences between ambient and canopy climate and leaf temperature. A path analysis was performed to quantify the interactions between components of the greenhouse canopy-climate system. We found that with high radiation the canopy climate can be up to 5°C cooler than the ambient climate, while for cloudy days this was only 2°C. Canopy relative humidity (RH) was up to 25% higher compared to ambient RH. We showed that radiation is very important for these climate differences, but that this effect could be partly counteracted by turning off supplementary light (i.e. due to its indirect effects e.g. changing light distribution). Leaf temperature was substantially different, both higher and lower, from the canopy air temperature. This difference was determined by leaf area index (LAI), temperature of the heating pipe and the use of supplementary light, which all strongly influence radiation, either shortwave or thermal radiation. The difference between leaf and ambient air temperature could be decreased by decreasing the LAI or increasing the temperature of the heating pipe.
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Affiliation(s)
- A. van Westreenen
- Horticulture and Product Physiology Group, Wageningen University and Research, Wageningen, The Netherlands
- Centre for Crop System Analysis, Wageningen University and Research, Wageningen, The Netherlands
- * E-mail: (AW); (LM)
| | - N. Zhang
- Horticulture and Product Physiology Group, Wageningen University and Research, Wageningen, The Netherlands
- Centre for Crop System Analysis, Wageningen University and Research, Wageningen, The Netherlands
| | - J. C. Douma
- Centre for Crop System Analysis, Wageningen University and Research, Wageningen, The Netherlands
- Laboratory of Entomology, Wageningen University and Research, Wageningen, The Netherlands
| | - J. B. Evers
- Centre for Crop System Analysis, Wageningen University and Research, Wageningen, The Netherlands
| | - N. P. R. Anten
- Centre for Crop System Analysis, Wageningen University and Research, Wageningen, The Netherlands
| | - L. F. M. Marcelis
- Horticulture and Product Physiology Group, Wageningen University and Research, Wageningen, The Netherlands
- * E-mail: (AW); (LM)
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Rong M, Zheng X, Ye M, Bai J, Xie X, Jin Y, He X. Phenotypic Plasticity of Staphylococcus aureus in Liquid Medium Containing Vancomycin. Front Microbiol 2019; 10:809. [PMID: 31057516 PMCID: PMC6477096 DOI: 10.3389/fmicb.2019.00809] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 03/29/2019] [Indexed: 12/17/2022] Open
Abstract
Phenotypic plasticity enables individuals to develop different phenotypes in a changing environment and promotes adaptive evolution. Genome-wide association study (GWAS) facilitates the study of the genetic basis of bacterial phenotypes, and provides a new opportunity for bacterial phenotypic plasticity research. To investigate the relationship between growth plasticity and genotype in bacteria, 41 Staphylococcus aureus strains, including 29 vancomycin-intermediate S. aureus (VISA) strains, were inoculated in the absence or presence of vancomycin for 48 h. Growth curves and maximum growth rates revealed that strains with the same minimum inhibitory concentration (MIC) showed different levels of plasticity in response to vancomycin. A bivariate GWAS was performed to map single-nucleotide polymorphisms (SNPs) associated with growth plasticity. In total, 227 SNPs were identified from 14 time points, while 15 high-frequency SNPs were mapped to different annotated genes. The P-values and growth variations between the two cultures suggest that non-coding region (SNP 738836), ebh (SNP 1394043), drug transporter (SNP 264897), and pepV (SNP 1775112) play important roles in the growth plasticity of S. aureus. Our study provides an alternative strategy for dissecting the adaptive growth of S. aureus in vancomycin and highlights the feasibility of bivariate GWAS in bacterial phenotypic plasticity research.
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Affiliation(s)
- Mengdi Rong
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xuyang Zheng
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Meixia Ye
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.,Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jun Bai
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xiangming Xie
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yi Jin
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xiaoqing He
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
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Drake JE, Vårhammar A, Kumarathunge D, Medlyn BE, Pfautsch S, Reich PB, Tissue DT, Ghannoum O, Tjoelker MG. A common thermal niche among geographically diverse populations of the widely distributed tree species Eucalyptus tereticornis: No evidence for adaptation to climate-of-origin. GLOBAL CHANGE BIOLOGY 2017; 23:5069-5082. [PMID: 28544671 DOI: 10.1111/gcb.13771] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 02/25/2017] [Indexed: 05/24/2023]
Abstract
Impacts of climate warming depend on the degree to which plants are constrained by adaptation to their climate-of-origin or exhibit broad climatic suitability. We grew cool-origin, central and warm-origin provenances of Eucalyptus tereticornis in an array of common temperature environments from 18 to 35.5°C to determine if this widely distributed tree species consists of geographically contrasting provenances with differentiated and narrow thermal niches, or if provenances share a common thermal niche. The temperature responses of photosynthesis, respiration, and growth were equivalent across the three provenances, reflecting a common thermal niche despite a 2,200 km geographic distance and 13°C difference in mean annual temperature at seed origin. The temperature dependence of growth was primarily mediated by changes in leaf area per unit plant mass, photosynthesis, and whole-plant respiration. Thermal acclimation of leaf, stem, and root respiration moderated the increase in respiration with temperature, but acclimation was constrained at high temperatures. We conclude that this species consists of provenances that are not differentiated in their thermal responses, thus rejecting our hypothesis of adaptation to climate-of-origin and suggesting a shared thermal niche. In addition, growth declines with warming above the temperature optima were driven by reductions in whole-plant leaf area and increased respiratory carbon losses. The impacts of climate warming will nonetheless vary across the geographic range of this and other such species, depending primarily on each provenance's climate position on the temperature response curves for photosynthesis, respiration, and growth.
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Affiliation(s)
- John E Drake
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Angelica Vårhammar
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Dushan Kumarathunge
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Belinda E Medlyn
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Sebastian Pfautsch
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Peter B Reich
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
- Department of Forest Resources, University of Minnesota, St. Paul, MN, USA
| | - David T Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Oula Ghannoum
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Mark G Tjoelker
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
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