1
|
Kazarina A, Sarkar S, Thapa S, Heeren L, Kamke A, Ward K, Hartung E, Ran Q, Galliart M, Jumpponen A, Johnson L, Lee STM. Home-field advantage affects the local adaptive interaction between Andropogon gerardii ecotypes and root-associated bacterial communities. Microbiol Spectr 2023; 11:e0020823. [PMID: 37606438 PMCID: PMC10580881 DOI: 10.1128/spectrum.00208-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 07/05/2023] [Indexed: 08/23/2023] Open
Abstract
Due to climate change, drought frequencies and severities are predicted to increase across the United States. Plant responses and adaptation to stresses depend on plant genetic and environmental factors. Understanding the effect of those factors on plant performance is required to predict species' responses to environmental change. We used reciprocal gardens planted with distinct regional ecotypes of the perennial grass Andropogon gerardii adapted to dry, mesic, and wet environments to characterize their rhizosphere communities using 16S rRNA metabarcode sequencing. Even though the local microbial pool was the main driver of these rhizosphere communities, the significant plant ecotypic effect highlighted active microbial recruitment in the rhizosphere, driven by ecotype or plant genetic background. Our data also suggest that ecotypes planted at their homesites were more successful in recruiting rhizosphere community members that were unique to the location. The link between the plants' homesite and the specific local microbes supported the "home field advantage" hypothesis. The unique homesite microbes may represent microbial specialists that are linked to plant stress responses. Furthermore, our data support ecotypic variation in the recruitment of congeneric but distinct bacterial variants, highlighting the nuanced plant ecotype effects on rhizosphere microbiome recruitment. These results improve our understanding of the complex plant host-soil microbe interactions and should facilitate further studies focused on exploring the functional potential of recruited microbes. Our study has the potential to aid in predicting grassland ecosystem responses to climate change and impact restoration management practices to promote grassland sustainability. IMPORTANCE In this study, we used reciprocal gardens located across a steep precipitation gradient to characterize rhizosphere communities of distinct dry, mesic, and wet regional ecotypes of the perennial grass Andropogon gerardii. We used 16S rRNA amplicon sequencing and focused oligotyping analysis and showed that even though location was the main driver of the microbial communities, ecotypes could potentially recruit distinct bacterial populations. We showed that different A. gerardii ecotypes were more successful in overall community recruitment and recruitment of microbes unique to the "home" environment, when growing at their "home site." We found evidence for "home-field advantage" interactions between the host and host-root-associated bacterial communities, and the capability of ecotypes to recruit specialized microbes that were potentially linked to plant stress responses. Our study aids in a better understanding of the factors that affect plant adaptation, improve management strategies, and predict grassland function under the changing climate.
Collapse
Affiliation(s)
- Anna Kazarina
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Soumyadev Sarkar
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Shiva Thapa
- Department of Biology, University of North Carolina, Greensboro, North Carolina, USA
| | - Leah Heeren
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Abgail Kamke
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Kaitlyn Ward
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Eli Hartung
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Qinghong Ran
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Matthew Galliart
- Department of Biological Sciences, Fort Hays State University, Hays, Kansas, USA
| | - Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Loretta Johnson
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Sonny T. M. Lee
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| |
Collapse
|
2
|
Gao B, Chen M, Oliver MJ. Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics. Int J Mol Sci 2023; 24:ijms24076708. [PMID: 37047681 PMCID: PMC10095079 DOI: 10.3390/ijms24076708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 03/31/2023] [Indexed: 04/07/2023] Open
Abstract
The post-transcriptional regulation of gene expression, in particular alternative splicing (AS) events, substantially contributes to the complexity of eukaryotic transcriptomes and proteomes [...]
Collapse
Affiliation(s)
- Bei Gao
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Moxian Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Melvin J. Oliver
- Division of Plant Sciences and Interdisciplinary Group, University of Missouri, Columbia, MO 65211, USA
| |
Collapse
|
3
|
Zhao Y, Zhang F, Mickan B, Wang D. Inoculation of wheat with Bacillus sp. wp-6 altered amino acid and flavonoid metabolism and promoted plant growth. PLANT CELL REPORTS 2023; 42:165-179. [PMID: 36348065 DOI: 10.1007/s00299-022-02947-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
Inoculation of wheat seedling with Bacillus sp. wp-6 changed amino acid metabolism and flavonoid synthesis and promoted plant growth. Plant growth-promoting rhizobacteria (PGPR), which can reduce the use of agrochemicals, is vital for the development of sustainable agriculture. In this study, proteomics and metabolomics analyses were performed to investigate the effects of inoculation with a PGPR, Bacillus sp. wp-6, on wheat (Triticum aestivum L.) seedling growth. The results showed that inoculation with Bacillus sp. wp-6 increased shoot and root fresh weights by 19% and 18%, respectively, after 40 days. The expression levels of alpha-linolenic acid metabolism-related proteins and metabolites (lipoxygenase 2, allene oxide synthase 2, jasmonic acid, 17-hydroxylinolenic acid) and flavonoid biosynthesis-related proteins and metabolites (chalcone synthase 2 and PHC 4'-O-glucoside) were up-regulated. In addition, the expression levels of amino acid metabolism-related proteins (NADH-dependent glutamate synthase, bifunctional aspartokinase/homoserine, anthranilate synthase alpha subunit 1, and 3-phosphoshikimate 1-carboxyvinyltransferase) and metabolites (L-aspartate, L-arginine, and S-glutathionyl-L-cysteine) were also significantly up-regulated. Among them, NADH-dependent glutamate synthase and bifunctional aspartokinase/homoserine could act as regulators of nitrogen metabolism. Overall, inoculation of wheat with Bacillus sp. wp-6 altered alpha-linolenic acid metabolism, amino acid metabolism, and flavonoid synthesis and promoted wheat seedling growth. This study will deepen our understanding of the mechanism by which Bacillus sp. wp-6 promotes wheat growth using proteomics and metabolomics.
Collapse
Affiliation(s)
- Yaguang Zhao
- Key Laboratory of Oasis Ecological Agriculture of Xinjiang Production and Construction Corps, Shihezi University, North 4th Street No. 221, Shihezi, 832003, Xinjiang, China
| | - Fenghua Zhang
- Key Laboratory of Oasis Ecological Agriculture of Xinjiang Production and Construction Corps, Shihezi University, North 4th Street No. 221, Shihezi, 832003, Xinjiang, China.
| | - Bede Mickan
- Institute of Agriculture, School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6001, Australia
| | - Dan Wang
- Key Laboratory of Oasis Ecological Agriculture of Xinjiang Production and Construction Corps, Shihezi University, North 4th Street No. 221, Shihezi, 832003, Xinjiang, China
| |
Collapse
|
4
|
Kichko AA, Gladkov GV, Ulianich PS, Safronova VI, Pinaev AG, Sekste EA, Belimov AA, Andronov EE. Water Stress, Cadmium, and Plant Genotype Modulate the Rhizosphere Microbiome of Pisum sativum L. PLANTS (BASEL, SWITZERLAND) 2022; 11:3013. [PMID: 36432739 PMCID: PMC9699616 DOI: 10.3390/plants11223013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/19/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
Drought and heavy metals seriously affect plant growth and the biodiversity of the associated rhizosphere microbiomes, which, in turn, could be involved in the adaptation of plants to these environmental stresses. Rhizosphere soil was collected from a three-factor pot experiment, where pea line SGE and its Cd-tolerant mutant SGECdt were cultivated under both optimal and limited water conditions and treated with a toxic Cd concentration. The taxonomic structure of the prokaryotic rhizosphere microbiome was analyzed with the high-throughput sequencing of 16S rRNA amplicon libraries. A permutation test demonstrated statistically significant effects of Cd and water stress but not of pea genotype on the rhizosphere microbiome structure. Phylogenetic isometric log-ratio data transformation identified the taxonomic balances that were affected by abiotic factors and pea genotypes. A small number of significant (log ratio [-3.0:+3.0]) and phylogenetically deep balances characterized water stress, while a larger number of weak (log ratio [-0.8:+0.8]) phylogenetically lower balances described the influence of the plant genotype. Stress caused by cadmium took on an intermediate position. The main conclusion of the study is that the most powerful factor affecting the rhizosphere microbiome was water stress, and the weakest factor was plant genotype since it demonstrated a very weak transformation of the taxonomic structure of rhizosphere microbiomes in terms of alpha diversity indices, beta diversity, and the log ratio values of taxonomic balances.
Collapse
Affiliation(s)
- Arina A. Kichko
- All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh. 3, Pushkin, 196608 Saint-Petersburg, Russia
| | - Grigory V. Gladkov
- All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh. 3, Pushkin, 196608 Saint-Petersburg, Russia
| | - Pavel S. Ulianich
- All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh. 3, Pushkin, 196608 Saint-Petersburg, Russia
| | - Vera I. Safronova
- All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh. 3, Pushkin, 196608 Saint-Petersburg, Russia
| | - Alexander G. Pinaev
- All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh. 3, Pushkin, 196608 Saint-Petersburg, Russia
| | - Edgar A. Sekste
- All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh. 3, Pushkin, 196608 Saint-Petersburg, Russia
| | - Andrey A. Belimov
- All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh. 3, Pushkin, 196608 Saint-Petersburg, Russia
| | - Evgeny E. Andronov
- All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh. 3, Pushkin, 196608 Saint-Petersburg, Russia
- Dokuchaev Soil Science Institute, 119017 Moscow, Russia
| |
Collapse
|