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Bray SM, Hämälä T, Zhou M, Busoms S, Fischer S, Desjardins SD, Mandáková T, Moore C, Mathers TC, Cowan L, Monnahan P, Koch J, Wolf EM, Lysak MA, Kolar F, Higgins JD, Koch MA, Yant L. Kinetochore and ionomic adaptation to whole-genome duplication in Cochlearia shows evolutionary convergence in three autopolyploids. Cell Rep 2024; 43:114576. [PMID: 39116207 DOI: 10.1016/j.celrep.2024.114576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 05/17/2024] [Accepted: 07/18/2024] [Indexed: 08/10/2024] Open
Abstract
Whole-genome duplication (WGD) occurs in all kingdoms and impacts speciation, domestication, and cancer outcome. However, doubled DNA management can be challenging for nascent polyploids. The study of within-species polyploidy (autopolyploidy) permits focus on this DNA management aspect, decoupling it from the confounding effects of hybridization (in allopolyploid hybrids). How is autopolyploidy tolerated, and how do young polyploids stabilize? Here, we introduce a powerful model to address this: the genus Cochlearia, which has experienced many polyploidization events. We assess meiosis and other polyploid-relevant phenotypes, generate a chromosome-scale genome, and sequence 113 individuals from 33 ploidy-contrasting populations. We detect an obvious autopolyploidy-associated selection signal at kinetochore components and ion transporters. Modeling the selected alleles, we detail evidence of the kinetochore complex mediating adaptation to polyploidy. We compare candidates in independent autopolyploids across three genera separated by 40 million years, highlighting a common function at the process and gene levels, indicating evolutionary flexibility in response to polyploidy.
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Affiliation(s)
- Sian M Bray
- The University of Nottingham, Nottingham NG7 2RD, UK; The John Innes Centre, Norwich NR4 7UH, UK
| | - Tuomas Hämälä
- The University of Nottingham, Nottingham NG7 2RD, UK
| | - Min Zhou
- The University of Nottingham, Nottingham NG7 2RD, UK
| | - Silvia Busoms
- The John Innes Centre, Norwich NR4 7UH, UK; Department of Plant Physiology, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Sina Fischer
- The University of Nottingham, Nottingham NG7 2RD, UK
| | - Stuart D Desjardins
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Terezie Mandáková
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Chris Moore
- The University of Nottingham, Nottingham NG7 2RD, UK
| | - Thomas C Mathers
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Laura Cowan
- The University of Nottingham, Nottingham NG7 2RD, UK
| | | | | | - Eva M Wolf
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Martin A Lysak
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Filip Kolar
- Department of Botany, Charles University, Benátská 2, 12801 Prague, Czech Republic; The Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
| | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Marcus A Koch
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Levi Yant
- The University of Nottingham, Nottingham NG7 2RD, UK; Department of Botany, Charles University, Benátská 2, 12801 Prague, Czech Republic.
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Abdelfadil MR, Patz S, Kolb S, Ruppel S. Unveiling the influence of salinity on bacterial microbiome assembly of halophytes and crops. ENVIRONMENTAL MICROBIOME 2024; 19:49. [PMID: 39026296 PMCID: PMC11256479 DOI: 10.1186/s40793-024-00592-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 07/07/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND Climate change and anthropogenic activities intensify salinity stress impacting significantly on plant productivity and biodiversity in agroecosystems. There are naturally salt-tolerant plants (halophytes) that can grow and withstand such harsh conditions. Halophytes have evolved along with their associated microbiota to adapt to hypersaline environments. Identifying shared microbial taxa between halophyte species has rarely been investigated. We performed a comprehensive meta-analysis using the published bacterial 16S rRNA gene sequence datasets to untangle the rhizosphere microbiota structure of two halophyte groups and non-halophytes. We aimed for the identification of marker taxa of plants being adapted to a high salinity using three independent approaches. RESULTS Fifteen studies met the selection criteria for downstream analysis, consisting of 40 plants representing diverse halophyte and non-halophyte species. Microbiome structural analysis revealed distinct compositions for halophytes that face high salt concentrations in their rhizosphere compared to halophytes grown at low salt concentrations or from non-halophytes. For halophytes grown at high salt concentrations, we discovered three bacterial genera that were independently detected through the analysis of the core microbiome, key hub taxa by network analysis and random forest analysis. These genera were Thalassospira, Erythrobacter, and Marinobacter. CONCLUSIONS Our meta-analysis revealed that salinity level is a critical factor in affecting the rhizosphere microbiome assembly of plants. Detecting marker taxa across high-halophytes may help to select Bacteria that might improve the salt tolerance of non-halophytic plants.
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Affiliation(s)
- Mohamed R Abdelfadil
- Thaer-Institute, Faculty of Life Sciences, Humboldt University of Berlin, 10115, Berlin, Germany.
- Department of Plant-Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), 14979, Großbeeren, Germany.
- Microbial Biogeochemistry, RA Landscape Functioning, Leibniz Center for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374, Müncheberg, Germany.
| | - Sascha Patz
- Computomics GmbH, Eisenbahnstraße 1, 72072, Tübingen, Baden-Württemberg, Germany
| | - Steffen Kolb
- Thaer-Institute, Faculty of Life Sciences, Humboldt University of Berlin, 10115, Berlin, Germany
- Microbial Biogeochemistry, RA Landscape Functioning, Leibniz Center for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374, Müncheberg, Germany
| | - Silke Ruppel
- Department of Plant-Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), 14979, Großbeeren, Germany
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Prathaban M, Prathiviraj R, Ravichandran M, Natarajan SD, Sobanaa M, Hari Krishna Kumar S, Chandrasekar V, Selvin J. Isoptericola haloaureus sp. nov., a dimorphic actinobacterium isolated from mangrove sediments of southeast India, implicating biosaline agricultural significance through nitrogen fixation and salt tolerance genes. Antonie Van Leeuwenhoek 2024; 117:89. [PMID: 38861000 DOI: 10.1007/s10482-024-01985-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/25/2024] [Indexed: 06/12/2024]
Abstract
Strain MP-1014T, an obligate halophilic actinobacterium, was isolated from the mangrove soil of Thandavarayancholanganpettai, Tamil Nadu, India. A polyphasic approach was utilized to explore its phylogenetic position completely. The isolate was Gram-positive, filamentous, non-motile, and coccoid in older cultures. Ideal growth conditions were seen at 30 °C and pH 7.0, with 5% NaCl (W/V), and the DNA G + C content was 73.3%. The phylogenic analysis of this strain based upon 16S rRNA gene sequence revealed 97-99.8% similarity to the recognized species of the genus Isoptericola. Strain MP-1014T exhibits the highest similarity to I. sediminis JC619T (99.7%), I. chiayiensis KCTC19740T (98.9%), and subsequently to I. halotolerans KCTC19646T (98.6%), when compared with other members within the Isoptericola genus (< 98%). ANI scores of strain MP-1014T are 86.4%, 84.2%, and 81.5% and dDDH values are 59.7%, 53.6%, and 34.8% with I. sediminis JC619T, I. chiayiensis KCTC19740T and I. halotolerans KCTC19646T respectively. The major polar lipids of the strain MP-1014T were phosphatidylinositol, phosphatidylglycerol, diphosphotidylglycerol, two unknown phospholipids, and glycolipids. The predominant respiratory menaquinones were MK9 (H4) and MK9 (H2). The major fatty acids were anteiso-C15:0, anteiso-C17:0, iso-C14:0, C15:0, and C16:0. Also, initial genome analysis of the organism suggests it as a biostimulant for enhancing agriculture in saline environments. Based on phenotypic and genetic distinctiveness, the strain MP-1014 T represents the novel species of the genus Isoptericola assigned Isoptericola haloaureus sp. nov., is addressed by the strain MP-1014 T, given its phenotypic, phylogenetic, and hereditary uniqueness. The type strain is MP-1014T [(NCBI = OP672482.1 = GCA_036689775.1) ATCC = BAA 2646T; DSMZ = 29325T; MTCC = 13246T].
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Affiliation(s)
- Munisamy Prathaban
- Department of Microbiology, Pondicherry University, Puducherry, 605014, India.
| | | | - Mythili Ravichandran
- Department of Microbiology, Vivekanandha Arts and Science College for Women, Sankagiri, Tamil Nadu, India
| | - Sharmila Devi Natarajan
- School of Biosciences, Mar Athanasios College for Advanced Studies, Thiruvalla, Kerala, India
| | - Murugesan Sobanaa
- Department of Microbiology, Pondicherry University, Puducherry, 605014, India
| | | | | | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Puducherry, 605014, India
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Bontpart T, Weiss A, Vile D, Gérard F, Lacombe B, Reichheld JP, Mari S. Growing on calcareous soils and facing climate change. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00069-4. [PMID: 38570279 DOI: 10.1016/j.tplants.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 04/05/2024]
Abstract
Soil calcium carbonate (CaCO3) impacts plant mineral nutrition far beyond Fe metabolism, imposing constraints for crop growth and quality in calcareous agrosystems. Our knowledge on plant strategies to tolerate CaCO3 effects mainly refers to Fe acquisition. This review provides an update on plant cellular and molecular mechanisms recently described to counteract the negative effects of CaCO3 in soils, as well as recent efforts to identify genetic bases involved in CaCO3 tolerance from natural populations, that could be exploited to breed CaCO3-tolerant crops. Finally, we review the impact of environmental factors (soil water content, air CO2, and temperature) affecting soil CaCO3 equilibrium and plant tolerance to calcareous soils, and we propose strategies for improvement in the context of climate change.
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Affiliation(s)
- Thibaut Bontpart
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Alizée Weiss
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
| | - Denis Vile
- LEPSE, INRAE, Institut Agro, Université de Montpellier, 2 Place P. Viala, F-34060, Montpellier cédex 2, France
| | - Frédéric Gérard
- UMR Eco&Sols, INRAE, IRD, CIRAD, Institut Agro, Université de Montpellier, Montpellier, France
| | - Benoît Lacombe
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | | | - Stéphane Mari
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France.
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Damankeshan B, Shamshiri MH, Alaei H. Endophytic fungi are able to induce tolerance to salt stress in date palm seedlings (Phoenix dactylifera L.). Braz J Microbiol 2024; 55:759-775. [PMID: 38157149 PMCID: PMC10920517 DOI: 10.1007/s42770-023-01216-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024] Open
Abstract
Date palm, typically considered a salinity-resistant plant, grows in arid and semi-arid regions worldwide, and experiences decreased growth and yields under salt stress. This study investigates the efficacy of endophytic fungi (EF) in enhancing the salinity tolerance of date palm seedlings. In this experiment, EF were isolated from date tree roots and identified morphologically. Following molecular identification, superior strains were selected to inoculate date palm seedlings (Phoenix dactylifera L., cv. Mazafati). The seedlings were subjected to varying levels of salinity stress for 4 months, utilizing a completely randomized factorial design with two factors: fungal strain type (six levels) and salinity stress (0, 100, 200, and 300 mM sodium chloride). The diversity analysis of endophytic fungi in date palm trees revealed that the majority of isolates belonged to the Ascomycota family, with Fusarium and Alternaria being the most frequently isolated genera. In this research, the application of fungal endophytes resulted in increased dry weight of roots, shoots, root length, plant height, and leaf number. Additionally, EF symbiosis with date palm seedling roots led to a reduction in sodium concentration and an increase in potassium and phosphorus concentrations in aerial parts under salt-stress conditions. While salinity elevated lipid peroxidation, consequently increasing malondialdehyde (MDA) levels, EF mitigated damage from reactive oxygen species (ROS) by enhancing antioxidant enzyme activity, including superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX), while promoting proline and total soluble sugar (TSS) accumulation. The colonization percentage generally increased with salinity stress intensity in most strains. According to the results, the application of EF can alleviate the adverse effects of salinity stress and enhance the growth of date palm seedlings under saline conditions.
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Affiliation(s)
- Bahareh Damankeshan
- Department of Horticultural Science, College of Agriculture, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran.
| | - Mohammad Hosein Shamshiri
- Department of Horticultural Science, College of Agriculture, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
| | - Hosein Alaei
- Department of Plant Pathology, College of Agriculture, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
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