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Compant S, Cassan F, Kostić T, Johnson L, Brader G, Trognitz F, Sessitsch A. Harnessing the plant microbiome for sustainable crop production. Nat Rev Microbiol 2024:10.1038/s41579-024-01079-1. [PMID: 39147829 DOI: 10.1038/s41579-024-01079-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2024] [Indexed: 08/17/2024]
Abstract
Global research on the plant microbiome has enhanced our understanding of the complex interactions between plants and microorganisms. The structure and functions of plant-associated microorganisms, as well as the genetic, biochemical, physical and metabolic factors that influence the beneficial traits of plant microbiota have also been intensively studied. Harnessing the plant microbiome has led to the development of various microbial applications to improve crop productivity in the face of a range of challenges, for example, climate change, abiotic and biotic stresses, and declining soil properties. Microorganisms, particularly nitrogen-fixing rhizobia as well as mycorrhizae and biocontrol agents, have been applied for decades to improve plant nutrition and health. Still, there are limitations regarding efficacy and consistency under field conditions. Also, the wealth of expanding knowledge on microbiome diversity, functions and interactions represents a huge source of information to exploit for new types of application. In this Review, we explore plant microbiome functions, mechanisms, assembly and types of interaction, and discuss current applications and their pitfalls. Furthermore, we elaborate on how the latest findings in plant microbiome research may lead to the development of new or more advanced applications. Finally, we discuss research gaps to fully leverage microbiome functions for sustainable plant production.
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Affiliation(s)
| | | | - Tanja Kostić
- AIT Austrian Institute of Technology, Vienna, Austria
| | | | - Günter Brader
- AIT Austrian Institute of Technology, Vienna, Austria
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Hussain A, Faizan S, Kumari R, Pandey E. Morphological and biochemical responses of Vicia faba (faba beans) grown on fly ash amended soil in the presence of Rhizobium leguminosarum and arbuscular mycorrhizal fungus. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:44361-44373. [PMID: 38949734 DOI: 10.1007/s11356-024-34154-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 06/24/2024] [Indexed: 07/02/2024]
Abstract
An experiment was conducted in the greenhouse to investigate the feasibility of Vicia faba grown on different fly ash concentrations (0-30%) and dual inoculation with Rhizobium and arbuscular mycorrhizal fungi (AMF). Sampling was done 45 days after sowing to analyse the plant growth parameters, photosynthetic attributes (total chlorophyll and carotenoids content), protein content, nitrogen (N) and phosphorus (P) content, defensive factors (antioxidant activity and proline content) and damage markers (lipid peroxidation, reactive oxygen species and cell viability). The results revealed that the application of fly ash (FA) alone did not result in any significant improvement in growth, biochemical and physiological parameters. However, dual inoculation showed a synergistic impact on legume growth, photosynthetic pigments, protein, proline, and cell viability. Rhizobium, AMF and 10% FA showed maximum enhancement in all attributes mentioned. 20% and 30% fly doses showed a reduction in growth, photosynthesis and antioxidants and caused oxidative stress via lipid peroxidation. The results showed that the synergistic or combined interactions between all three variables of the symbiotic relationship (Rhizobium-legume-AMF) boosted plant productivity.
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Affiliation(s)
- Alisha Hussain
- Environmental Physiology Laboratory, Department of Botany, Aligarh Muslim University, U.P, Aligarh, 202002, India
| | - Shahla Faizan
- Environmental Physiology Laboratory, Department of Botany, Aligarh Muslim University, U.P, Aligarh, 202002, India.
| | - Rinkee Kumari
- Environmental Physiology Laboratory, Department of Botany, Aligarh Muslim University, U.P, Aligarh, 202002, India
| | - Ekta Pandey
- Environmental Physiology Laboratory, Department of Botany, Aligarh Muslim University, U.P, Aligarh, 202002, India
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Wang C, Zhang Y, Wang S, Lv X, Xu J, Zhang X, Yang Q, Meng F, Xu B. Differential effects of domesticated and wild Capsicum frutescens L. on microbial community assembly and metabolic functions in rhizosphere soil. Front Microbiol 2024; 15:1383526. [PMID: 39040904 PMCID: PMC11261347 DOI: 10.3389/fmicb.2024.1383526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/20/2024] [Indexed: 07/24/2024] Open
Abstract
Objective Rhizosphere microorganisms play crucial roles in the growth and development of plants, disease resistance, and environmental adaptability. As the only wild pepper variety resource in China, domesticated Capsicum frutescens Linn. (Xiaomila) exhibits varying beneficial traits and affects rhizosphere microbial composition compared with its wild counterparts. In this study, we aimed to identify specific rhizosphere microbiome and metabolism patterns established during the domestication process. Methods The rhizosphere microbial diversity and composition of domesticated and wild C. frutescens were detected and analyzed by metagenomics. Non-targeted metabolomics were used to explore the differences of metabolites in rhizosphere soil between wild and domesticated C. frutescens. Results We found that the rhizosphere microbial diversity of domesticated variety was significantly different from that of the wild variety, with Massilia being its dominant bacteria. However, the abundance of certain beneficial microbes such as Gemmatimonas, Streptomyces, Rambibacter, and Lysobacter decreased significantly. The main metabolites identified in the wild variety included serylthreonine, deoxyloganic acid, vitamin C, among others. In contrast, those identified in the domesticated group were 4-hydroxy-l-glutamic acid and benzoic acid. Furthermore, the differentially enriched pathways were concentrated in tyrosine and tryptophan biosynthesis, histidine and purine-derived alkaloids biosynthesis, benzoic acid family, two-component system, etc. Conclusion This study revealed that C. frutescens established specific rhizosphere microbiota and metabolites during domestication, which has important significance for the efficient utilization of beneficial microorganisms in breeding and cultivation practices.
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Affiliation(s)
- Can Wang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
- Institute of Medicinal Biological Technique, Wenshan Academy of Agricultural Sciences, Wenshan, Yunnan, China
| | - Yinghua Zhang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Shaoxiang Wang
- Institute of Medicinal Biological Technique, Wenshan Academy of Agricultural Sciences, Wenshan, Yunnan, China
| | - Xia Lv
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Junqiang Xu
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xueting Zhang
- Institute of Medicinal Biological Technique, Wenshan Academy of Agricultural Sciences, Wenshan, Yunnan, China
| | - Qing Yang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Fanlai Meng
- College of Biological and Agricultural Sciences, Honghe University, Mengzi, Yunnan, China
| | - Bin Xu
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
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Bouznif B, Boukherissa A, Jaszczyszyn Y, Mars M, Timchenko T, Shykoff JA, Alunni B. Complete and circularized genome sequences of five nitrogen-fixing Bradyrhizobium sp. strains isolated from root nodules of peanut, Arachis hypogaea, cultivated in Tunisia. Microbiol Resour Announc 2024; 13:e0107823. [PMID: 38747611 PMCID: PMC11237496 DOI: 10.1128/mra.01078-23] [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: 11/13/2023] [Accepted: 04/15/2024] [Indexed: 06/12/2024] Open
Abstract
This manuscript reports the complete and circularized Oxford Nanopore Technologies (ONT) long read-based genome sequences of five nitrogen-fixing symbionts belonging to the genus Bradyrhizobium, isolated from root nodules of peanut (Arachis hypogaea) grown on soil samples collected from Tunisia.
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Affiliation(s)
- Besma Bouznif
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- IDEEV—Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTech Université Paris-Saclay, Gif-sur-Yvette, France
- Research Unit Biodiversity and Valorization of Arid Areas Bioresources (BVBAA), Faculty of Sciences, Gabès, Tunisia
- Université de Picardie Jules Verne, UMRt BioEcoAgro 1158-INRAE, BIOPI, Amiens, France
| | - Amira Boukherissa
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- IDEEV—Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTech Université Paris-Saclay, Gif-sur-Yvette, France
| | - Yan Jaszczyszyn
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Mohamed Mars
- Research Unit Biodiversity and Valorization of Arid Areas Bioresources (BVBAA), Faculty of Sciences, Gabès, Tunisia
| | - Tatiana Timchenko
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Jacqui A. Shykoff
- IDEEV—Laboratoire Ecologie, Systématique et Evolution, CNRS, AgroParisTech Université Paris-Saclay, Gif-sur-Yvette, France
| | - Benoît Alunni
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
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Calderon RB, Dangi SR. Arbuscular Mycorrhizal Fungi and Rhizobium Improve Nutrient Uptake and Microbial Diversity Relative to Dryland Site-Specific Soil Conditions. Microorganisms 2024; 12:667. [PMID: 38674611 PMCID: PMC11052256 DOI: 10.3390/microorganisms12040667] [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: 03/08/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) and rhizobium play a significant role in plant symbiosis. However, their influence on the rhizosphere soil microbiome associated with nutrient acquisition and soil health is not well defined in the drylands of Montana (MT), USA. This study investigated the effect of microbial inoculants as seed treatment on pea yield, nutrient uptake, potential microbial functions, and rhizosphere soil microbial communities using high-throughput sequencing of 16S and ITS rRNA genes. The experiment was conducted under two contrasting dryland conditions with four treatments: control, single inoculation with AMF or Rhizobium, and dual inoculations of AMF and Rhizobium (AMF+Rhizobium). Our findings revealed that microbial inoculation efficacy was site-specific. AMF+Rhizobium synergistically increased grain yield at Sidney dryland field site (DFS) 2, while at Froid site, DFS 1, AMF improved plant resilience to acidic soil but contributed a marginal yield under non-nutrient limiting conditions. Across dryland sites, the plants' microbial dependency on AMF+Rhizobium (12%) was higher than single inoculations of AMF (8%) or Rhizobium (4%) alone. Variations in microbial community structure and composition indicate a site-specific response to AMF and AMF+Rhizobium inoculants. Overall, site-specific factors significantly influenced plant nutrient uptake, microbial community dynamics, and functional potential. It underscores the need for tailored management strategies that consider site-specific characteristics to optimize benefits from microbial inoculation.
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Affiliation(s)
- Rosalie B. Calderon
- Agricultural Research Service, Northern Plains Agricultural Research Laboratory, USDA, 1500 N Central Avenue, Sidney, MT 59270, USA
| | - Sadikshya R. Dangi
- Correspondence: (R.B.C.); (S.R.D.); Tel.: +1-(406)-433-9479 (R.B.C.); +1-(406)-433-9490 (S.R.D.); Fax: +1-(406)-433-5038 (R.B.C. & S.R.D.)
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Zorin EA, Sulima AS, Zhernakov AI, Kuzmina DO, Rakova VA, Kliukova MS, Romanyuk DA, Kulaeva OA, Akhtemova GA, Shtark OY, Tikhonovich IA, Zhukov VA. Genomic and Transcriptomic Analysis of Pea ( Pisum sativum L.) Breeding Line 'Triumph' with High Symbiotic Responsivity. PLANTS (BASEL, SWITZERLAND) 2023; 13:78. [PMID: 38202386 PMCID: PMC10781049 DOI: 10.3390/plants13010078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
Pea (Pisum sativum L.), like most legumes, forms mutualistic symbioses with nodule bacteria and arbuscular mycorrhizal (AM) fungi. The positive effect of inoculation is partially determined by the plant genotype; thus, pea varieties with high and low symbiotic responsivity have been described, but the molecular genetic basis of this trait remains unknown. Here, we compare the symbiotically responsive breeding line 'Triumph' of grain pea with its parental cultivars 'Vendevil' (a donor of high symbiotic responsivity) and 'Classic' (a donor of agriculturally valuable traits) using genome and transcriptome sequencing. We show that 'Triumph' inherited one-fourth of its genome from 'Vendevil', including the genes related to AM and nodule formation, and reveal that under combined inoculation with nodule bacteria and AM fungi, 'Triumph' and 'Vendevil', in contrast to 'Classic', demonstrate similar up-regulation of the genes related to solute transport, hormonal regulation and flavonoid biosynthesis in their roots. We also identify the gene PsGLP2, whose expression pattern distinguishing 'Triumph' and 'Vendevil' from 'Classic' correlates with difference within the promoter region sequence, making it a promising marker for the symbiotic responsivity trait. The results of this study may be helpful for future molecular breeding programs aimed at creation of symbiotically responsive cultivars of pea.
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Affiliation(s)
- Evgeny A. Zorin
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Anton S. Sulima
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Aleksandr I. Zhernakov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Daria O. Kuzmina
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Valeria A. Rakova
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius 354340, Russia;
| | - Marina S. Kliukova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Daria A. Romanyuk
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Olga A. Kulaeva
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Gulnar A. Akhtemova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Oksana Y. Shtark
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Igor A. Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius 354340, Russia;
| | - Vladimir A. Zhukov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius 354340, Russia;
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Liang R, Liu JL, Ji XQ, Olsen KM, Qiang S, Song XL. Fitness and Hard Seededness of F 2 and F 3 Descendants of Hybridization between Herbicide-Resistant Glycine max and G. soja. PLANTS (BASEL, SWITZERLAND) 2023; 12:3671. [PMID: 37960027 PMCID: PMC10650743 DOI: 10.3390/plants12213671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023]
Abstract
The commercial cultivation of herbicide-resistant (HR) transgenic soybeans (Glycine max L. Merr.) raises great concern that transgenes may introgress into wild soybeans (Glycine soja Sieb. et Zucc.) via pollen-mediated gene flow, which could increase the ecological risks of transgenic weed populations and threaten the genetic diversity of wild soybean. To assess the fitness of hybrids derived from transgenic HR soybean and wild soybean, the F2 and F3 descendants of crosses of the HR soybean line T14R1251-70 and two wild soybeans (LNTL and JLBC, which were collected from LiaoNing TieLing and JiLin BaiCheng, respectively), were planted along with their parents in wasteland or farmland soil, with or without weed competition. The fitness of F2 and F3 was significantly increased compared to the wild soybeans under all test conditions, and they also showed a greater competitive ability against weeds. Seeds produced by F2 and F3 were superficially similar to wild soybeans in having a hard seed coat; however, closer morphological examination revealed that the hard-seededness was lower due to the seed coat structure, specifically the presence of thicker hourglass cells in seed coat layers and lower Ca content in palisade epidermis. Hybrid descendants containing the cp4-epsps HR allele were able to complete their life cycle and produce a large number of seeds in the test conditions, which suggests that they would be able to survive in the soil beyond a single growing season, germinate, and grow under suitable conditions. Our findings indicate that the hybrid descendants of HR soybean and wild soybean may pose potential ecological risks in regions of soybean cultivation where wild soybean occurs.
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Affiliation(s)
- Rong Liang
- Weed Research Laboratory, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (R.L.); (J.-L.L.); (X.-Q.J.); (S.Q.)
| | - Jia-Li Liu
- Weed Research Laboratory, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (R.L.); (J.-L.L.); (X.-Q.J.); (S.Q.)
| | - Xue-Qin Ji
- Weed Research Laboratory, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (R.L.); (J.-L.L.); (X.-Q.J.); (S.Q.)
| | - Kenneth M. Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA;
| | - Sheng Qiang
- Weed Research Laboratory, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (R.L.); (J.-L.L.); (X.-Q.J.); (S.Q.)
| | - Xiao-Ling Song
- Weed Research Laboratory, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (R.L.); (J.-L.L.); (X.-Q.J.); (S.Q.)
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Signaling and Detoxification Strategies in Plant-Microbes Symbiosis under Heavy Metal Stress: A Mechanistic Understanding. Microorganisms 2022; 11:microorganisms11010069. [PMID: 36677361 PMCID: PMC9865731 DOI: 10.3390/microorganisms11010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
Plants typically interact with a variety of microorganisms, including bacteria, mycorrhizal fungi, and other organisms, in their above- and below-ground parts. In the biosphere, the interactions of plants with diverse microbes enable them to acquire a wide range of symbiotic advantages, resulting in enhanced plant growth and development and stress tolerance to toxic metals (TMs). Recent studies have shown that certain microorganisms can reduce the accumulation of TMs in plants through various mechanisms and can reduce the bioavailability of TMs in soil. However, relevant progress is lacking in summarization. This review mechanistically summarizes the common mediating pathways, detoxification strategies, and homeostatic mechanisms based on the research progress of the joint prevention and control of TMs by arbuscular mycorrhizal fungi (AMF)-plant and Rhizobium-plant interactions. Given the importance of tripartite mutualism in the plant-microbe system, it is necessary to further explore key signaling molecules to understand the role of plant-microbe mutualism in improving plant tolerance under heavy metal stress in the contaminated soil environments. It is hoped that our findings will be useful in studying plant stress tolerance under a broad range of environmental conditions and will help in developing new technologies for ensuring crop health and performance in future.
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Microbial endophytes: application towards sustainable agriculture and food security. Appl Microbiol Biotechnol 2022; 106:5359-5384. [PMID: 35902410 DOI: 10.1007/s00253-022-12078-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 02/06/2023]
Abstract
Microbial endophytes are ubiquitous and exist in each recognised plant species reported till date. Within the host plant, the entire community of microbes lives non-invasively within the active internal tissues without causing any harm to the plant. Endophytes interact with their host plant via metabolic communication enables them to generate signal molecules. In addition, the host plant's genetic recombination with endophytes helps them to imitate the host's physicochemical functions and develop identical active molecules. Therefore, when cultured separately, they begin producing the host plant phytochemicals. The fungal species Penicillium chrysogenum has portrayed the glory days of antibiotics with the invention of the antibiotic penicillin. Therefore, fungi have substantially supported social health by developing many bioactive molecules utilised as antioxidant, antibacterial, antiviral, immunomodulatory and anticancerous agents. But plant-related microbes have emanated as fountainheads of biologically functional compounds with higher levels of medicinal perspective in recent years. Researchers have been motivated by the endless need for potent drugs to investigate alternate ways to find new endophytes and bioactive molecules, which tend to be a probable aim for drug discovery. The current research trends with these promising endophytic organisms are reviewed in this review paper. KEY POINTS: • Identified 54 important bioactive compounds as agricultural relevance • Role of genome mining of endophytes and "Multi-Omics" tools in sustainable agriculture • A thorough description and graphical presentation of agricultural significance of plant endophytes.
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Zhou J, Wilson GWT, Cobb AB, Zhang Y, Liu L, Zhang X, Sun F. Mycorrhizal and rhizobial interactions influence model grassland plant community structure and productivity. MYCORRHIZA 2022; 32:15-32. [PMID: 35037106 DOI: 10.1007/s00572-021-01061-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/24/2021] [Indexed: 05/20/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi and rhizobium are likely important drivers of plant coexistence and grassland productivity due to complementary roles in supplying limiting nutrients. However, the interactive effects of mycorrhizal and rhizobial associations on plant community productivity and competitive dynamics remain unclear. To address this, we conducted a greenhouse experiment to determine the influences of these key microbial functional groups on communities comprising three plant species by comparing plant communities grown with or without each symbiont. We also utilized N-fertilization and clipping treatments to explore potential shifts in mycorrhizal and rhizobial benefits across abiotic and biotic conditions. Our research suggests AM fungi and rhizobium co-inoculation was strongly facilitative for plant community productivity and legume (Medicago sativa) growth and nodulation. Plant competitiveness shifted in the presence of AM fungi and rhizobium, favoring M. sativa over a neighboring C4 grass (Andropogon gerardii) and C3 forb (Ratibida pinnata). This may be due to rhizobial symbiosis as well as the relatively greater mycorrhizal growth response of M. sativa, compared to the other model plants. Clipping and N-fertilization altered relative costs and benefits of both symbioses, presumably by altering host-plant nitrogen and carbon dynamics, leading to a relative decrease in mycorrhizal responsiveness and proportional biomass of M. sativa relative to the total biomass of the entire plant community, with a concomitant relative increase in A. gerardii and R. pinnata proportional biomass. Our results demonstrate a strong influence of both microbial symbioses on host-plant competitiveness and community dynamics across clipping and N-fertilization treatments, suggesting the symbiotic rhizosphere community is critical for legume establishment in grasslands.
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Affiliation(s)
- Jiqiong Zhou
- Department of Grassland Science, College of Grassland Science & Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
- Department of Grassland Science, College of Grassland Science & Technology, China Agricultural University, Beijing, China.
| | - Gail W T Wilson
- Department of Natural Resource Ecology and Management, Oklahoma State University, Stillwater, OK, 008C AGH74078, USA
| | - Adam B Cobb
- Department of Natural Resource Ecology and Management, Oklahoma State University, Stillwater, OK, 008C AGH74078, USA
| | - Yingjun Zhang
- Department of Grassland Science, College of Grassland Science & Technology, China Agricultural University, Beijing, China
| | - Lin Liu
- Department of Grassland Science, College of Grassland Science & Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xinquan Zhang
- Department of Grassland Science, College of Grassland Science & Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Feida Sun
- Department of Grassland Science, College of Grassland Science & Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
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Allelic Diversity at Abiotic Stress Responsive Genes in Relationship to Ecological Drought Indices for Cultivated Tepary Bean, Phaseolus acutifolius A. Gray, and Its Wild Relatives. Genes (Basel) 2021; 12:genes12040556. [PMID: 33921270 PMCID: PMC8070098 DOI: 10.3390/genes12040556] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/01/2021] [Accepted: 04/09/2021] [Indexed: 12/22/2022] Open
Abstract
Some of the major impacts of climate change are expected in regions where drought stress is already an issue. Grain legumes are generally drought susceptible. However, tepary bean and its wild relatives within Phaseolus acutifolius or P. parvifolius are from arid areas between Mexico and the United States. Therefore, we hypothesize that these bean accessions have diversity signals indicative of adaptation to drought at key candidate genes such as: Asr2, Dreb2B, and ERECTA. By sequencing alleles of these genes and comparing to estimates of drought tolerance indices from climate data for the collection site of geo-referenced, tepary bean accessions, we determined the genotype x environmental association (GEA) of each gene. Diversity analysis found that cultivated and wild P. acutifolius were intermingled with var. tenuifolius and P. parvifolius, signifying that allele diversity was ample in the wild and cultivated clade over a broad sense (sensu lato) evaluation. Genes Dreb2B and ERECTA harbored signatures of directional selection, represented by six SNPs correlated with the environmental drought indices. This suggests that wild tepary bean is a reservoir of novel alleles at genes for drought tolerance, as expected for a species that originated in arid environments. Our study corroborated that candidate gene approach was effective for marker validation across a broad genetic base of wild tepary accessions.
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Oladzad A, González A, Macchiavelli R, de Jensen CE, Beaver J, Porch T, McClean P. Genetic Factors Associated With Nodulation and Nitrogen Derived From Atmosphere in a Middle American Common Bean Panel. FRONTIERS IN PLANT SCIENCE 2020; 11:576078. [PMID: 33384700 PMCID: PMC7769817 DOI: 10.3389/fpls.2020.576078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
Among grain legume crops, common beans (Phaseolus vulgaris L.) are considered to have poor biological nitrogen (N2) fixation (BNF) capabilities although variation in N2 fixing capabilities exists within the species. The availability of genetic panel varying in BNF capacity and a large-scale single nucleotide polymorphism (SNP) data set for common bean provided an opportunity to discover genetic factors associated with N2 fixation among genotypes in the Middle American gene pool. Using nodulation and percentage of N2-derived from atmosphere (%NDFA) data collected from field trials, at least 11 genotypes with higher levels of BNF capacity were identified. Genome-wide association studies (GWASs) detected both major and minor effects that control these traits. A major nodulation interval at Pv06:28.0-28.27 Mbp was discovered. In this interval, the peak SNP was located within a small GTPase that positively regulates cellular polarity and growth of root hair tips. Located 20 kb upstream of this peak SNP is an auxin-responsive factor AUX/indole acetic auxin (IAA)-related gene involved in auxin transportation during root nodulation. For %NDFA, nitrate (NO3 -) transporters, NRT1:2 and NRT1.7 (Pv02:8.64), squamosa promoter binding transcriptome factor (Pv08:28.42), and multi-antimicrobial extrusion protein (MATE) efflux family protein (Pv06:10.91) were identified as candidate genes. Three additional QTLs were identified on chromosomes Pv03:5.24, Pv09:25.89, and Pv11: 32.89 Mbp. These key candidate genes from both traits were integrated with previous results on N2 fixation to describe a BNF pathway.
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Affiliation(s)
- Atena Oladzad
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Abiezer González
- Department of Agroenvironmental Sciences, University of Puerto Rico, Mayagüez, Puerto Rico
| | - Raul Macchiavelli
- Department of Agroenvironmental Sciences, University of Puerto Rico, Mayagüez, Puerto Rico
| | | | - James Beaver
- Department of Agroenvironmental Sciences, University of Puerto Rico, Mayagüez, Puerto Rico
| | - Tim Porch
- USDA-ARS, Tropical Agriculture Research Station, Mayagüez, Puerto Rico
| | - Phillip McClean
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
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Ku YS, Cheng SS, Gerhardt A, Cheung MY, Contador CA, Poon LYW, Lam HM. Secretory Peptides as Bullets: Effector Peptides from Pathogens against Antimicrobial Peptides from Soybean. Int J Mol Sci 2020; 21:E9294. [PMID: 33291499 PMCID: PMC7730307 DOI: 10.3390/ijms21239294] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 12/24/2022] Open
Abstract
Soybean is an important crop as both human food and animal feed. However, the yield of soybean is heavily impacted by biotic stresses including insect attack and pathogen infection. Insect bites usually make the plants vulnerable to pathogen infection, which causes diseases. Fungi, oomycetes, bacteria, viruses, and nematodes are major soybean pathogens. The infection by pathogens and the defenses mounted by soybean are an interactive and dynamic process. Using fungi, oomycetes, and bacteria as examples, we will discuss the recognition of pathogens by soybean at the molecular level. In this review, we will discuss both the secretory peptides for soybean plant infection and those for pathogen inhibition. Pathogenic secretory peptides and peptides secreted by soybean and its associated microbes will be included. We will also explore the possible use of externally applied antimicrobial peptides identical to those secreted by soybean and its associated microbes as biopesticides.
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Affiliation(s)
- Yee-Shan Ku
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong; (Y.-S.K.); (S.-S.C.); (A.G.); (M.-Y.C.); (C.A.C.); (L.-Y.W.P.)
| | - Sau-Shan Cheng
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong; (Y.-S.K.); (S.-S.C.); (A.G.); (M.-Y.C.); (C.A.C.); (L.-Y.W.P.)
| | - Aisha Gerhardt
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong; (Y.-S.K.); (S.-S.C.); (A.G.); (M.-Y.C.); (C.A.C.); (L.-Y.W.P.)
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Ming-Yan Cheung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong; (Y.-S.K.); (S.-S.C.); (A.G.); (M.-Y.C.); (C.A.C.); (L.-Y.W.P.)
| | - Carolina A. Contador
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong; (Y.-S.K.); (S.-S.C.); (A.G.); (M.-Y.C.); (C.A.C.); (L.-Y.W.P.)
| | - Lok-Yiu Winnie Poon
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong; (Y.-S.K.); (S.-S.C.); (A.G.); (M.-Y.C.); (C.A.C.); (L.-Y.W.P.)
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong; (Y.-S.K.); (S.-S.C.); (A.G.); (M.-Y.C.); (C.A.C.); (L.-Y.W.P.)
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