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Nytko AG, Hord AM, Senior JK, O’Reilly-Wapstra J, Schweitzer JA, Bailey JK. Evolution of rarity and phylogeny determine above- and belowground biomass in plant-plant interactions. PLoS One 2024; 19:e0294839. [PMID: 38768148 PMCID: PMC11104619 DOI: 10.1371/journal.pone.0294839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/22/2024] [Indexed: 05/22/2024] Open
Abstract
Rare species are often considered inferior competitors due to occupancy of small ranges, specific habitats, and small local populations. However, the phylogenetic relatedness and rarity level (level 1-7 and common) of interacting species in plant-plant interactions are not often considered when predicting the response of rare plants in a biotic context. We used a common garden of 25 species of Tasmanian Eucalyptus, to differentiate non-additive patterns in the biomass of rare versus common species when grown in mixtures varying in phylogenetic relatedness and rarity. We demonstrate that rare species maintain progressively positive non-additive responses in biomass when interacting with phylogenetically intermediate, less rare and common species. This trend is not reflected in common species that out-performed in monocultures compared to mixtures. These results offer predictability as to how rare species' productivity will respond within various plant-plant interactions. However, species-specific interactions, such as those involving E. globulus, yielded a 97% increase in biomass compared to other species-specific interaction outcomes. These results are important because they suggest that plant rarity may also be shaped by biotic interactions, in addition to the known environmental and population factors normally used to describe rarity. Rare species may utilize potentially facilitative interactions with phylogenetically intermediate and common species to escape the effects of limiting similarity. Biotically mediated increases in rare plant biomass may have subsequent effects on the competitive ability and geographic occurrence of rare species, allowing rare species to persist at low abundance across plant communities. Through the consideration of species rarity and evolutionary history, we can more accurately predict plant-plant interaction dynamics to preserve unique ecosystem functions and fundamentally challenge what it means to be "rare".
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Affiliation(s)
- Alivia G. Nytko
- Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, United States of America
| | - Ashlynn M. Hord
- Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, United States of America
| | - John K. Senior
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Tasmania, Australia
| | - Julianne O’Reilly-Wapstra
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Tasmania, Australia
| | - Jennifer A. Schweitzer
- Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, United States of America
| | - Joseph K. Bailey
- Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, United States of America
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Lucero JE, Filazzola A, Callaway RM, Braun J, Ghazian N, Haas S, Miguel MF, Owen M, Seifan M, Zuliani M, Lortie CJ. Increasing global aridity destabilizes shrub facilitation of exotic but not native plant species. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Yang X, Yu H, Duncan S, Zhang Y, Cheema J, Liu H, Benjamin Miller J, Zhang J, Kwok CK, Zhang H, Ding Y. RNA G-quadruplex structure contributes to cold adaptation in plants. Nat Commun 2022; 13:6224. [PMID: 36266343 PMCID: PMC9585020 DOI: 10.1038/s41467-022-34040-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/11/2022] [Indexed: 12/24/2022] Open
Abstract
Nucleotide composition is suggested to infer gene functionality and ecological adaptation of species to distinct environments. However, the underlying biological function of nucleotide composition dictating environmental adaptations is largely unknown. Here, we systematically analyze the nucleotide composition of transcriptomes across 1000 plants (1KP) and their corresponding habitats. Intriguingly, we find that plants growing in cold climates have guanine (G)-enriched transcriptomes, which are prone to forming RNA G-quadruplex structures. Both immunofluorescence detection and in vivo structure profiling reveal that RNA G-quadruplex formation in plants is globally enhanced in response to cold. Cold-responsive RNA G-quadruplexes strongly enhanced mRNA stability, rather than affecting translation. Disruption of individual RNA G-quadruplex promotes mRNA decay in the cold, leading to impaired plant cold response. Therefore, we propose that plants adopted RNA G-quadruplex structure as a molecular signature to facilitate their adaptation to the cold during evolution.
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Affiliation(s)
- Xiaofei Yang
- grid.27446.330000 0004 1789 9163Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024 China ,grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China ,grid.9227.e0000000119573309CAS-JIC Center of Excellence for Plant and Microbial Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China ,grid.14830.3e0000 0001 2175 7246Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom
| | - Haopeng Yu
- grid.27446.330000 0004 1789 9163Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024 China ,grid.14830.3e0000 0001 2175 7246Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom
| | - Susan Duncan
- grid.14830.3e0000 0001 2175 7246Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom
| | - Yueying Zhang
- grid.14830.3e0000 0001 2175 7246Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom
| | - Jitender Cheema
- grid.14830.3e0000 0001 2175 7246Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom
| | - Haifeng Liu
- grid.14830.3e0000 0001 2175 7246Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom ,grid.440622.60000 0000 9482 4676State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018 China
| | - J. Benjamin Miller
- grid.8273.e0000 0001 1092 7967School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ United Kingdom
| | - Jie Zhang
- grid.14830.3e0000 0001 2175 7246Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom
| | - Chun Kit Kwok
- grid.35030.350000 0004 1792 6846Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China ,grid.35030.350000 0004 1792 6846Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057 China
| | - Huakun Zhang
- grid.27446.330000 0004 1789 9163Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024 China
| | - Yiliang Ding
- grid.14830.3e0000 0001 2175 7246Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom
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Brooker R, Brown LK, George TS, Pakeman RJ, Palmer S, Ramsay L, Schöb C, Schurch N, Wilkinson MJ. Active and adaptive plasticity in a changing climate. TRENDS IN PLANT SCIENCE 2022; 27:717-728. [PMID: 35282996 DOI: 10.1016/j.tplants.2022.02.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/24/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Better understanding of the mechanistic basis of plant plasticity will enhance efforts to breed crops resilient to predicted climate change. However, complexity in plasticity's conceptualisation and measurement may hinder fruitful crossover of concepts between disciplines that would enable such advances. We argue active adaptive plasticity is particularly important in shaping the fitness of wild plants, representing the first line of a plant's defence to environmental change. Here, we define how this concept may be applied to crop breeding, suggest appropriate approaches to measure it in crops, and propose a refocussing on active adaptive plasticity to enhance crop resilience. We also discuss how the same concept may have wider utility, such as in ex situ plant conservation and reintroductions.
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Affiliation(s)
- Rob Brooker
- Department of Ecological Sciences, James Hutton Institute, Aberdeen, UK; Department of Ecological Sciences, James Hutton Institute, Dundee, UK.
| | - Lawrie K Brown
- Department of Ecological Sciences, James Hutton Institute, Dundee, UK
| | - Timothy S George
- Department of Ecological Sciences, James Hutton Institute, Dundee, UK
| | - Robin J Pakeman
- Department of Ecological Sciences, James Hutton Institute, Aberdeen, UK
| | - Sarah Palmer
- Institute of Biological, Environmental, and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, Ceredigion, UK
| | - Luke Ramsay
- Department of Ecological Sciences, James Hutton Institute, Dundee, UK
| | - Christian Schöb
- Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | | | - Mike J Wilkinson
- Institute of Biological, Environmental, and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, Ceredigion, UK
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Zhang LY, Xing ZT, Chen LQ, Zhang XJ, Fan SJ. Comprehensive Time-Course Transcriptome and Co-expression Network Analyses Identify Salt Stress Responding Mechanisms in Chlamydomonas reinhardtii Strain GY-D55. FRONTIERS IN PLANT SCIENCE 2022; 13:828321. [PMID: 35283918 PMCID: PMC8908243 DOI: 10.3389/fpls.2022.828321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
It is highly necessary to understand the molecular mechanism underlying the salt stress response in green algae, which may contribute to finding the evolutionary cues of abiotic stress response in plants. Here, we reported a comprehensive temporal investigation of transcriptomes using data at eight different time points, from an early stage (2 h) to a late stage (up to 96 h) in Chlamydomonas reinhardtii GY-D55 cells. The principal component analysis (PCA) of transcriptome profiles showed that the samples of the early and late stages were well separated. A total of 12,445 genes were detected as differentially expressed genes. There were 1,861/2,270 common upregulated/downregulated genes for each time point compared with control samples. Samples treated with salt for 2, 8, and 24 h had a relatively large number of characteristic upregulated/downregulated genes. The functional enrichment analysis highlighted the timing of candidate regulatory mechanisms for salt stress responses in GY-D55 cells. Short time exposure to salt stress impaired oxidation-reduction, protein synthesis and modification, and photosynthesis. The algal cells promoted transcriptional regulation and protein folding to deal with protein synthesis/modification impairments and rapidly accumulated glycerol in the early stage (2-4 h) to cope with osmotic stress. At 12 and 24 h, GY-D55 cells showed increased expressions of signaling and photosynthetic genes to deal with the damage of photosynthesis. The co-expression module blue was predicted to regulate endoplasmic reticulum (ER) stress at early time points. In addition, we identified a total of 113 transcription factors (TFs) and predicted the potential roles of Alfin, C2C2, and the MYB family TFs in algal salt stress response.
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