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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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Raio A, Brilli F, Neri L, Baraldi R, Orlando F, Pugliesi C, Chen X, Baccelli I. Stenotrophomonas rhizophila Ep2.2 inhibits growth of Botrytis cinerea through the emission of volatile organic compounds, restricts leaf infection and primes defense genes. FRONTIERS IN PLANT SCIENCE 2023; 14:1235669. [PMID: 37849842 PMCID: PMC10577304 DOI: 10.3389/fpls.2023.1235669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/05/2023] [Indexed: 10/19/2023]
Abstract
The bacterium Stenotrophomonas rhizophila is known to be beneficial for plants and has been frequently isolated from the rhizosphere of crops. In the present work, we isolated from the phyllosphere of an ornamental plant an epiphytic strain of S. rhizophila that we named Ep2.2 and investigated its possible application in crop protection. Compared to S. maltophilia LMG 958, a well-known plant beneficial species which behaves as opportunistic human pathogen, S. rhizophila Ep2.2 showed distinctive features, such as different motility, a generally reduced capacity to use carbon sources, a greater sensitivity to fusidic acid and potassium tellurite, and the inability to grow at the human body temperature. S. rhizophila Ep2.2 was able to inhibit in vitro growth of the plant pathogenic fungi Alternaria alternata and Botrytis cinerea through the emission of volatile compounds. Simultaneous PTR-MS and GC-MS analyses revealed the emission, by S. rhizophila Ep2.2, of volatile organic compounds (VOCs) with well-documented antifungal activity, such as furans, sulphur-containing compounds and terpenes. When sprayed on tomato leaves and plants, S. rhizophila Ep2.2 was able to restrict B. cinerea infection and to prime the expression of Pti5, GluA and PR1 plant defense genes.
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Affiliation(s)
- Aida Raio
- Institute for Sustainable Plant Protection (IPSP), National Research Council of Italy (CNR), Florence, Italy
| | - Federico Brilli
- Institute for Sustainable Plant Protection (IPSP), National Research Council of Italy (CNR), Florence, Italy
| | - Luisa Neri
- Institute for BioEconomy (IBE), National Research Council of Italy (CNR), Bologna, Italy
| | - Rita Baraldi
- Institute for BioEconomy (IBE), National Research Council of Italy (CNR), Bologna, Italy
| | - Francesca Orlando
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Xiaoyulong Chen
- College of Agriculture, College of Tobacco Science, Guizhou University, Guiyang, China
| | - Ivan Baccelli
- Institute for Sustainable Plant Protection (IPSP), National Research Council of Italy (CNR), Florence, Italy
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Ferreira MJ, Sierra-Garcia IN, Louvado A, Gomes NCM, Figueiredo S, Patinha C, Pinto DCGA, Cremades J, Silva H, Cunha Â. Domestication shapes the endophytic microbiome and metabolome of Salicornia europaea. J Appl Microbiol 2023; 134:lxad178. [PMID: 37587019 DOI: 10.1093/jambio/lxad178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/20/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023]
Abstract
AIMS We aim at understanding the effect of domestication on the endophytic microbiome and metabolome of Salicornia europaea and collecting evidence on the potential role of microbial populations and metabolites in the adaptation of plants to different ecological contexts (wild vs crops). METHODS AND RESULTS Samples were collected from a natural salt marsh (wild) and an intensive crop field (crop). High-throughput sequencing of the 16S rRNA gene, gas chromatography-mass spectrometry (GC-MS) and ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) were used to analyze the endophytic bacterial communities and the metabolite profiles of S. europaea roots, respectively. The elemental analysis of the plant shoots was performed by Inductively Coupled Plasma-Mass Spectroscopy (ICP-MS).Overall, significant differences were found between the microbiome of wild and cultivated plants. The later showed a higher relative abundance of the genera Erythrobacter, Rhodomicrobium, and Ilumatobacter than wild plants. The microbiome of wild plants was enriched in Marinobacter, Marixanthomonas, and Thalassospira. The metabolite profile of crop plants revealed higher amounts of saturated and non-saturated fatty acids and acylglycerols. In contrast, wild plants contained comparatively more carbohydrates and most macroelements (i.e. Na, K, Mg, and Ca). CONCLUSIONS There is a strong correlation between plant metabolites and the endosphere microbiome of S. europaea. In wild populations, plants were enriched in carbohydrates and the associated bacterial community was enriched in genes related to primary metabolic pathways such as nitrogen metabolism and carbon fixation. The endosphere microbiome of crop plants was predicted to have higher gene counts related to pathogenesis. Crop plants also exhibited higher amounts of azelaic acid, an indicator of exposure to phytopathogens.
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Affiliation(s)
- Maria J Ferreira
- Department of Biology & Center for Environmental and Marine Studies (CESAM), University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - I Natalia Sierra-Garcia
- Department of Biology & Center for Environmental and Marine Studies (CESAM), University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - António Louvado
- Department of Biology & Center for Environmental and Marine Studies (CESAM), University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Newton C M Gomes
- Department of Biology & Center for Environmental and Marine Studies (CESAM), University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Sandro Figueiredo
- Department of Biology & Center for Environmental and Marine Studies (CESAM), University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Carla Patinha
- Department of Geosciences & Geobiotec, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Diana C G A Pinto
- LAQV-REQUIMTE & Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Javier Cremades
- Centre for Advanced Scientific Research (CICA), University of A Coruña, 15071 A Coruña, Spain
| | - Helena Silva
- Department of Biology & Center for Environmental and Marine Studies (CESAM), University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Ângela Cunha
- Department of Biology & Center for Environmental and Marine Studies (CESAM), University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
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Xavier GR, Jesus EDC, Dias A, Coelho MRR, Molina YC, Rumjanek NG. Contribution of Biofertilizers to Pulse Crops: From Single-Strain Inoculants to New Technologies Based on Microbiomes Strategies. PLANTS (BASEL, SWITZERLAND) 2023; 12:954. [PMID: 36840302 PMCID: PMC9962295 DOI: 10.3390/plants12040954] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Pulses provide distinct health benefits due to their low fat content and high protein and fiber contents. Their grain production reaches approximately 93,210 × 103 tons per year. Pulses benefit from the symbiosis with atmospheric N2-fixing bacteria, which increases productivity and reduces the need for N fertilizers, thus contributing to mitigation of environmental impact mitigation. Additionally, the root region harbors a rich microbial community with multiple traits related to plant growth promotion, such as nutrient increase and tolerance enhancement to abiotic or biotic stresses. We reviewed the eight most common pulses accounting for almost 90% of world production: common beans, chickpeas, peas, cowpeas, mung beans, lentils, broad beans, and pigeon peas. We focused on updated information considering both single-rhizobial inoculation and co-inoculation with plant growth-promoting rhizobacteria. We found approximately 80 microbial taxa with PGPR traits, mainly Bacillus sp., B. subtilis, Pseudomonas sp., P. fluorescens, and arbuscular mycorrhizal fungi, and that contributed to improve plant growth and yield under different conditions. In addition, new data on root, nodule, rhizosphere, and seed microbiomes point to strategies that can be used to design new generations of biofertilizers, highlighting the importance of microorganisms for productive pulse systems.
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Affiliation(s)
| | | | - Anelise Dias
- Departamento de Fitotecnia, Instituto de Agronomia, Universidade Federal Rural do Rio de Janeiro, UFRRJ, Rodovia BR-465, Km 7, Seropédica 23890-000, RJ, Brazil
| | | | - Yulimar Castro Molina
- Programa de Pós-graduação em Microbiologia Agrícola, Universidade Federal de Lavras, UFLA, Trevo Rotatório Professor Edmir Sá Santos, Lavras 37203-202, MG, Brazil
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Yin Y, Wang YF, Cui HL, Zhou R, Li L, Duan GL, Zhu YG. Distinctive Structure and Assembly of Phyllosphere Microbial Communities between Wild and Cultivated Rice. Microbiol Spectr 2023; 11:e0437122. [PMID: 36625666 PMCID: PMC9927517 DOI: 10.1128/spectrum.04371-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/16/2022] [Indexed: 01/11/2023] Open
Abstract
Wild rice has been demonstrated to possess enriched genetic diversity and multiple valuable traits involved in disease/pest resistance and abiotic stress tolerance, which provides a potential resource for sustainable agriculture. However, unlike the plant compartments such as rhizosphere, the structure and assembly of phyllosphere microbial communities of wild rice remain largely unexplored. Through amplicon sequencing, this study compared the phyllosphere bacterial and fungal communities of wild rice and its neighboring cultivated rice. The core phyllosphere microbial taxa of both wild and cultivated rice are dominated with Pantoea, Methylobacterium, Nigrospora, and Papiliotrema, which are potentially beneficial to rice growth and health. Compared to the cultivated rice, Methylobacterium, Sphingomonas, Phaeosphaeria, and Khuskia were significantly enriched in the wild rice phyllosphere. The potentially nitrogen-fixing Methylobacterium is the dominated wild-enriched microbe; Sphingomonas is the hub taxon of wild rice networks. In addition, the microbiota of wild rice was more governed by deterministic assembly with a more complicated and stable community network than the cultivated rice. Our study provides a list of the beneficial microbes in the wild rice phyllosphere and reveals the microbial divergence between wild rice and cultivated rice in the original habitats, which highlights the potential selective role of wild rice in recruiting specific microbiomes for enhancing crop performance and promoting sustainable food production. IMPORTANCE Plant microbiota are being considered a lever to increase the sustainability of food production under a changing climate. In particular, the microbiomes associated with ancestors of modern cultivars have the potential to support their domesticated cultivars. However, few efforts have been devoted to studying the biodiversity and functions of microbial communities in the native habitats of ancestors of modern crop species. This study provides a list of the beneficial microbes in the wild rice phyllosphere and explores the microbial interaction patterns and the functional profiles of wild rice. This information could be useful for the future utilization of the plant microbiome to enhance crop performance and sustainability, especially in the framework of sustainable agroecosystems.
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Affiliation(s)
- Yue Yin
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yi-Fei Wang
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hui-Ling Cui
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui Zhou
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lv Li
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Gui-Lan Duan
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yong-Guan Zhu
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
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Niza-Costa M, Rodríguez-dos Santos AS, Rebelo-Romão I, Ferrer MV, Sequero López C, Vílchez JI. Geographically Disperse, Culturable Seed-Associated Microbiota in Forage Plants of Alfalfa ( Medicago sativa L.) and Pitch Clover ( Bituminaria bituminosa L.): Characterization of Beneficial Inherited Strains as Plant Stress-Tolerance Enhancers. BIOLOGY 2022; 11:biology11121838. [PMID: 36552347 PMCID: PMC9775229 DOI: 10.3390/biology11121838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
Agricultural production is being affected by increasingly harsh conditions caused by climate change. The vast majority of crops suffer growth and yield declines due to a lack of water or intense heat. Hence, commercial legume crops suffer intense losses of production (20-80%). This situation is even more noticeable in plants used as fodder for animals, such as alfalfa and pitch trefoil, since their productivity is linked not only to the number of seeds produced, but also to the vegetative growth of the plant itself. Thus, we decided to study the microbiota associated with their seeds in different locations on the Iberian Peninsula, with the aim of identifying culturable bacteria strains that have adapted to harsh environments and that can be used as biotreatments to improve plant growth and resistance to stress. As potentially inherited microbiota, they may also represent a treatment with medium- and long-term adaptative effects. Hence, isolated strains showed no clear relationship with their geographical sampling location, but had about 50% internal similarity with their model plants. Moreover, out of the 51 strains isolated, about 80% were capable of producing biofilms; around 50% produced mid/high concentrations of auxins and grew notably in ACC medium; only 15% were characterized as xerotolerant, while more than 75% were able to sporulate; and finally, 65% produced siderophores and more than 40% produced compounds to solubilize phosphates. Thus, Paenibacillus amylolyticus BB B2-A, Paenibacillus xylanexedens MS M1-C, Paenibacillus pabuli BB Oeiras A, Stenotrophomonas maltophilia MS M1-B and Enterobacter hormaechei BB B2-C strains were tested as plant bioinoculants in lentil plants (Lens culinaris Medik.), showing promising results as future treatments to improve plant growth under stressful conditions.
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Affiliation(s)
- Marla Niza-Costa
- iPlantMicro Lab, Instituto de Tecnologia Química e Biológica (ITQB)-NOVA, Oeiras, 2784-501 Lisboa, Portugal
| | | | - Inês Rebelo-Romão
- iPlantMicro Lab, Instituto de Tecnologia Química e Biológica (ITQB)-NOVA, Oeiras, 2784-501 Lisboa, Portugal
| | - María Victoria Ferrer
- iPlantMicro Lab, Instituto de Tecnologia Química e Biológica (ITQB)-NOVA, Oeiras, 2784-501 Lisboa, Portugal
| | - Cristina Sequero López
- GeoBioTec, Department of Earth Sciences, NOVA School of Sciences and Technology, Universidade NOVA de Lisboa (Campus de Caparica), 1070-312 Caparica, Portugal
| | - Juan Ignacio Vílchez
- iPlantMicro Lab, Instituto de Tecnologia Química e Biológica (ITQB)-NOVA, Oeiras, 2784-501 Lisboa, Portugal
- Correspondence:
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Wild Wheat Rhizosphere-Associated Plant Growth-Promoting Bacteria Exudates: Effect on Root Development in Modern Wheat and Composition. Int J Mol Sci 2022; 23:ijms232315248. [PMID: 36499572 PMCID: PMC9740669 DOI: 10.3390/ijms232315248] [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: 10/20/2022] [Revised: 11/15/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Diazotrophic bacteria isolated from the rhizosphere of a wild wheat ancestor, grown from its refuge area in the Fertile Crescent, were found to be efficient Plant Growth-Promoting Rhizobacteria (PGPR), upon interaction with an elite wheat cultivar. In nitrogen-starved plants, they increased the amount of nitrogen in the seed crop (per plant) by about twofold. A bacterial growth medium was developed to investigate the effects of bacterial exudates on root development in the elite cultivar, and to analyze the exo-metabolomes and exo-proteomes. Altered root development was observed, with distinct responses depending on the strain, for instance, with respect to root hair development. A first conclusion from these results is that the ability of wheat to establish effective beneficial interactions with PGPRs does not appear to have undergone systematic deep reprogramming during domestication. Exo-metabolome analysis revealed a complex set of secondary metabolites, including nutrient ion chelators, cyclopeptides that could act as phytohormone mimetics, and quorum sensing molecules having inter-kingdom signaling properties. The exo-proteome-comprised strain-specific enzymes, and structural proteins belonging to outer-membrane vesicles, are likely to sequester metabolites in their lumen. Thus, the methodological processes we have developed to collect and analyze bacterial exudates have revealed that PGPRs constitutively exude a highly complex set of metabolites; this is likely to allow numerous mechanisms to simultaneously contribute to plant growth promotion, and thereby to also broaden the spectra of plant genotypes (species and accessions/cultivars) with which beneficial interactions can occur.
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Attah FA, Lawal BA, Yusuf AB, Adedeji OJ, Folahan JT, Akhigbe KO, Roy T, Lawal AA, Ogah NB, Olorundare OE, Chamcheu JC. Nutritional and Pharmaceutical Applications of Under-Explored Knottin Peptide-Rich Phytomedicines. PLANTS (BASEL, SWITZERLAND) 2022; 11:3271. [PMID: 36501311 PMCID: PMC9737898 DOI: 10.3390/plants11233271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/02/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Phytomedicines reportedly rich in cystine knot peptides (Knottins) are found in several global diets, food/herbal supplements and functional foods. However, their knottin peptide content has largely been unexplored, notably for their emerging dual potentials at both the food and medicine space. The nutritional roles, biological targets and mechanism(s) of activity of these knotted peptides are largely unknown. Meanwhile, knottins have recently been unveiled as emerging peptide therapeutics and nutraceuticals of primary choice due to their broad spectrum of bioactivity, hyper stability, selective toxicity, impressive selectivity for biomolecular targets, and their bioengineering applications. In addition to their potential dietary benefits, some knottins have displayed desirable limited toxicity to human erythrocytes. In an effort to appraise what has been accomplished, unveil knowledge gaps and explore the future prospects of knottins, an elaborate review of the nutritional and pharmaceutical application of phytomedicines rich in knottins was carried out. Herein, we provide comprehensive data on common dietary and therapeutic knottins, the majority of which are poorly investigated in many food-grade phytomedicines used in different cultures and localities. Findings from this review should stimulate scientific interest to unveil novel dietary knottins and knottin-rich nutraceutical peptide drug candidates/leads with potential for future clinical application.
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Affiliation(s)
- Francis Alfred Attah
- Department of Pharmacognosy and Drug Development, Faculty of Pharmaceutical Sciences, University of Ilorin, Ilorin 240272, Nigeria
| | - Bilqis Abiola Lawal
- Department of Pharmacognosy and Drug Development, Faculty of Pharmaceutical Sciences, University of Ilorin, Ilorin 240272, Nigeria
| | - Abdulmalik Babatunde Yusuf
- Department of Pharmacognosy and Drug Development, Faculty of Pharmaceutical Sciences, University of Ilorin, Ilorin 240272, Nigeria
| | - Oluwakorede Joshua Adedeji
- Department of Pharmacognosy and Drug Development, Faculty of Pharmaceutical Sciences, University of Ilorin, Ilorin 240272, Nigeria
| | - Joy Temiloluwa Folahan
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana-Monroe, Monroe, LA 71209, USA
| | - Kelvin Oluwafemi Akhigbe
- Department of Pharmacognosy and Drug Development, Faculty of Pharmaceutical Sciences, University of Ilorin, Ilorin 240272, Nigeria
| | - Tithi Roy
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana-Monroe, Monroe, LA 71209, USA
| | - Azeemat Adeola Lawal
- Department of Pharmacognosy and Drug Development, Faculty of Pharmaceutical Sciences, University of Ilorin, Ilorin 240272, Nigeria
| | - Ngozi Blessing Ogah
- Department of Biotechnology, Ebonyi State University, Abakaliki 480101, Nigeria
| | | | - Jean Christopher Chamcheu
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana-Monroe, Monroe, LA 71209, USA
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Liang R, Ji X, Sheng Z, Liu J, Qiang S, Song X. Fitness and Rhizobacteria of F2, F3 Hybrids of Herbicide-Tolerant Transgenic Soybean and Wild Soybean. PLANTS (BASEL, SWITZERLAND) 2022; 11:3184. [PMID: 36432913 PMCID: PMC9693618 DOI: 10.3390/plants11223184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
The introduction of herbicide-tolerant (HT) transgenic soybeans (Glycine max (L.) Merr.) into farming systems raises great concern that transgenes may flow to endemic wild soybeans (Glycine soja Sieb. et Zucc.) via pollen, which may increase the ecological risks by increasing the fitness of hybrids under certain conditions and threaten the genetic diversity of wild soybean populations. In order to demonstrate the potential risk of gene flow from the HT soybean to the wild soybean, the fitness of F2 and F3 hybrids obtained from two wild soybean populations (HLJHRB-1, JSCZ) collected from China and the HT soybean was measured under farmland and wasteland soil conditions, as well as with or without weed competition. Compared with their wild progenitors, the F2 and F3 hybrids of HLJHRB-1 displayed a higher emergence rate, higher aboveground dry biomass, more pods and filled-seed plants, as well as better composite fitness under four planting conditions. The F2 and F3 hybrids of JSCZ also displayed a higher emergence rate, higher aboveground dry biomass, more pods, and more filled seeds per plant under mixed planting, whereas these characteristics were lower under pure planting conditions in wasteland and farmland soil. Therefore, the composite fitness of JSCZ hybrids was higher or lower depending on the planting conditions. Furthermore, the soil microbial communities of the F3 of HLJHRB-1, JSCZ, and the wild soybean were investigated with 16S rDNA sequencing, which showed that low alpha diversity of rhizobacteria was relative to high fitness, and Rhizobium played an important role in promoting F3 plant growth.
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Chandel A, Mann R, Kaur J, Tannenbaum I, Norton S, Edwards J, Spangenberg G, Sawbridge T. Australian native Glycine clandestina seed microbiota hosts a more diverse bacterial community than the domesticated soybean Glycine max. ENVIRONMENTAL MICROBIOME 2022; 17:56. [PMID: 36384698 PMCID: PMC9670509 DOI: 10.1186/s40793-022-00452-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Plant microbiome composition has been demonstrated to change during the domestication of wild plants and it is suggested that this has resulted in loss of plant beneficial microbes. Recently, the seed microbiome of native plants was demonstrated to harbour a more diverse microbiota and shared a common core microbiome with modern cultivars. In this study the composition of the seed-associated bacteria of Glycine clandestina is compared to seed-associated bacteria of Glycine max (soybean). RESULTS The seed microbiome of the native legume Glycine clandestina (crop wild relative; cwr) was more diverse than that of the domesticated Glycine max and was dominated by the bacterial class Gammaproteobacteria. Both the plant species (cwr vs domesticated) and individual seed accessions were identified as the main driver for this diversity and composition of the microbiota of all Glycine seed lots, with the effect of factor "plant species" exceeded that of "geographical location". A core microbiome was identified between the two Glycine species. A high percentage of the Glycine microbiome was unculturable [G. clandestina (80.8%) and G. max (75.5%)] with only bacteria of a high relative abundance being culturable under the conditions of this study. CONCLUSION Our results provided novel insights into the structure and diversity of the native Glycine clandestina seed microbiome and how it compares to that of the domesticated crop Glycine max. Beyond that, it also increased our knowledge of the key microbial taxa associated with the core Glycine spp. microbiome, both wild and domesticated. The investigation of this commonality and diversity is a valuable and essential tool in understanding the use of native Glycine spp. for the discovery of new microbes that would be of benefit to domesticated Glycine max cultivars or any other economically important crops. This study has isolated microbes from a crop wild relative that are now available for testing in G. max for beneficial phenotypes.
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Affiliation(s)
- Ankush Chandel
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.
| | - Ross Mann
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Jatinder Kaur
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Ian Tannenbaum
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Sally Norton
- Agriculture Victoria Research, Australian Grains Genebank, Horsham, VIC, 3400, Australia
| | - Jacqueline Edwards
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - German Spangenberg
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Timothy Sawbridge
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
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11
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May-Mutul CG, López-Garrido MA, O’Connor-Sánchez A, Peña-Ramírez YJ, Labrín-Sotomayor NY, Estrada-Medina H, Ferrer MM. Hidden Tenants: Microbiota of the Rhizosphere and Phyllosphere of Cordia dodecandra Trees in Mayan Forests and Homegardens. PLANTS (BASEL, SWITZERLAND) 2022; 11:3098. [PMID: 36432829 PMCID: PMC9699097 DOI: 10.3390/plants11223098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
During domestication, the selection of cultivated plants often reduces microbiota diversity compared with their wild ancestors. Microbiota in compartments such as the phyllosphere or rhizosphere can promote fruit tree health, growth, and development. Cordia dodecandra is a deciduous tree used by Maya people for its fruit and wood, growing, to date, in remnant forest fragments and homegardens (traditional agroforestry systems) in Yucatán. In this work, we evaluated the microbiota's alpha and beta diversity per compartment (phyllosphere and rhizosphere) and per population (forest and homegarden) in the Northeast and Southwest Yucatán regions. Eight composite DNA samples (per compartment/population/region combination) were amplified for 16S-RNA (bacteria) and ITS1-2 (fungi) and sequenced by Illumina MiSeq. Bioinformatic analyses were performed with QIIME and phyloseq. For bacteria and fungi, from 107,947 and 128,786 assembled sequences, 618 and 1092 operating taxonomic units (OTUs) were assigned, respectively. The alpha diversity of bacteria and fungi was highly variable among samples and was similar among compartments and populations. A significant species turnover among populations and regions was observed in the rhizosphere. The core microbiota from the phyllosphere was similar among populations and regions. Forests and homegarden populations are reservoirs of the C. dodecandra phyllosphere core microbiome and significant rhizosphere biodiversity.
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Affiliation(s)
- Carla G. May-Mutul
- Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Universidad Autónoma de Yucatán, Mérida 97313, Mexico
| | - Miguel A. López-Garrido
- Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Universidad Autónoma de Yucatán, Mérida 97313, Mexico
| | - Aileen O’Connor-Sánchez
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida 97205, Mexico
| | - Yuri J. Peña-Ramírez
- Departamento de Ciencias de la Sustentabilidad, El Colegio de la Frontera Sur Unidad Campeche, Lerma 24500, Mexico
| | - Natalia Y. Labrín-Sotomayor
- Departamento de Ciencias de la Sustentabilidad, El Colegio de la Frontera Sur Unidad Campeche, Lerma 24500, Mexico
| | - Héctor Estrada-Medina
- Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Universidad Autónoma de Yucatán, Mérida 97313, Mexico
| | - Miriam M. Ferrer
- Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Universidad Autónoma de Yucatán, Mérida 97313, Mexico
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12
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Nerva L, Sandrini M, Moffa L, Velasco R, Balestrini R, Chitarra W. Breeding toward improved ecological plant-microbiome interactions. TRENDS IN PLANT SCIENCE 2022; 27:1134-1143. [PMID: 35803843 DOI: 10.1016/j.tplants.2022.06.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 06/04/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Domestication processes, amplified by breeding programs, have allowed the selection of more productive genotypes and more suitable crop lines capable of coping with the changing climate. Notwithstanding these advancements, the impact of plant breeding on the ecology of plant-microbiome interactions has not been adequately considered yet. This includes the possible exploitation of beneficial plant-microbe interactions to develop crops with improved performance and better adaptability to any environmental scenario. Here we discuss the exploitation of customized synthetic microbial communities in agricultural systems to develop more sustainable breeding strategies based on the implementation of multiple interactions between plants and their beneficial associated microorganisms.
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Affiliation(s)
- Luca Nerva
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy; National Research Council of Italy - Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce, 73, 10135 Torino (TO), Italy
| | - Marco Sandrini
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy; University of Udine, Department of Agricultural, Food, Environmental and Animal Sciences, Via delle Scienze 206, 33100, Udine, (UD), Italy
| | - Loredana Moffa
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy; University of Udine, Department of Agricultural, Food, Environmental and Animal Sciences, Via delle Scienze 206, 33100, Udine, (UD), Italy
| | - Riccardo Velasco
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy
| | - Raffaella Balestrini
- National Research Council of Italy - Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce, 73, 10135 Torino (TO), Italy.
| | - Walter Chitarra
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy; National Research Council of Italy - Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce, 73, 10135 Torino (TO), Italy
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13
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Liu JQ, Chen SM, Zhang CM, Xu MJ, Xing K, Li CG, Li K, Zhang YQ, Qin S. Abundant and diverse endophytic bacteria associated with medicinal plant Arctium lappa L. and their potential for host plant growth promoting. Antonie Van Leeuwenhoek 2022; 115:1405-1420. [DOI: 10.1007/s10482-022-01785-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/11/2022] [Indexed: 10/31/2022]
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14
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Ramanan V, Mechery S, Sarkar IN. GenBank as a source to monitor and analyze Host-Microbiome data. Bioinformatics 2022; 38:4172-4177. [PMID: 35801940 PMCID: PMC9438952 DOI: 10.1093/bioinformatics/btac487] [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: 03/10/2022] [Revised: 06/08/2022] [Accepted: 07/07/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Microbiome datasets are often constrained by sequencing limitations. GenBank is the largest collection of publicly available DNA sequences, which is maintained by the National Center of Biotechnology Information (NCBI). The metadata of GenBank records are a largely understudied resource and may be uniquely leveraged to access the sum of prior studies focused on microbiome composition. Here, we developed a computational pipeline to analyze GenBank metadata, containing data on hosts, microorganisms and their place of origin. This work provides the first opportunity to leverage the totality of GenBank to shed light on compositional data practices that shape how microbiome datasets are formed as well as examine host-microbiome relationships. RESULTS The collected dataset contains multiple kingdoms of microorganisms, consisting of bacteria, viruses, archaea, protozoa, fungi, and invertebrate parasites, and hosts of multiple taxonomical classes, including mammals, birds and fish. A human data subset of this dataset provides insights to gaps in current microbiome data collection, which is biased towards clinically relevant pathogens. Clustering and phylogenic analysis reveals the potential to use these data to model host taxonomy and evolution, revealing groupings formed by host diet, environment and coevolution. AVAILABILITY AND IMPLEMENTATION GenBank Host-Microbiome Pipeline is available at https://github.com/bcbi/genbank_holobiome. The GenBank loader is available at https://github.com/bcbi/genbank_loader. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Vivek Ramanan
- Center of Computational Molecular Biology Brown University, Providence, RI, USA
- Center for Biomedical Informatics Brown University, Providence, RI, USA
| | - Shanti Mechery
- Center for Biomedical Informatics Brown University, Providence, RI, USA
| | - Indra Neil Sarkar
- Center of Computational Molecular Biology Brown University, Providence, RI, USA
- Center for Biomedical Informatics Brown University, Providence, RI, USA
- Rhode Island Quality Institute, Providence, RI, USA
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15
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Rincón-Molina CI, Martínez-Romero E, Aguirre-Noyola JL, Manzano-Gómez LA, Zenteno-Rojas A, Rogel MA, Rincón-Molina FA, Ruíz-Valdiviezo VM, Rincón-Rosales R. Bacterial Community with Plant Growth-Promoting Potential Associated to Pioneer Plants from an Active Mexican Volcanic Complex. Microorganisms 2022; 10:microorganisms10081568. [PMID: 36013987 PMCID: PMC9413462 DOI: 10.3390/microorganisms10081568] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/31/2022] [Accepted: 08/01/2022] [Indexed: 02/05/2023] Open
Abstract
Microorganisms in extreme volcanic environments play an important role in the development of plants on newly exposed substrates. In this work, we studied the structure and diversity of a bacterial community associated to Andropogon glomeratus and Cheilanthes aemula at El Chichón volcano. The genetic diversity of the strains was revealed by genomic fingerprints and by 16S rDNA gene sequencing. Furthermore, a metagenomic analysis of the rhizosphere samples was carried out for pioneer plants growing inside and outside the volcano. Multifunctional biochemical tests and plant inoculation assays were evaluated to determine their potential as plant growth-promoting bacteria (PGPB). Through metagenomic analysis, a total of 33 bacterial phyla were identified from A. glomeratus and C. aemula rhizosphere samples collected inside the volcano, and outside the volcano 23 bacterial phyla were identified. For both rhizosphere samples, proteobacteria was the most abundant phylum. With a cultivable approach, 174 bacterial strains were isolated from the rhizosphere and tissue of plants growing outside the volcanic complex. Isolates were classified within the genera Acinetobacter, Arthrobacter, Bacillus, Burkholderia, Cupriavidus, Enterobacter, Klebsiella, Lysinibacillus, Pantoea, Pseudomonas, Serratia, Stenotrophomonas and Pandoraea. The evaluated strains were able to produce indole compounds, solubilize phosphate, synthesize siderophores, showed ACC deaminase and nitrogenase activity, and they had a positive effect on the growth and development of Capsicum chinense. The wide diversity of bacteria associated to pioneer plants at El Chichón volcano with PGPB qualities represent an alternative for the recovery of eroded environments, and they can be used efficiently as biofertilizers for agricultural crops growing under adverse conditions.
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Affiliation(s)
- Clara Ivette Rincón-Molina
- Laboratorio de Ecología Genómica, Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, C.P., Tuxtla Gutierrez 29050, Chiapas, Mexico
| | - Esperanza Martínez-Romero
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, C.P., Cuernavaca 62210, Morelos, Mexico
| | - José Luis Aguirre-Noyola
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, C.P., Cuernavaca 62210, Morelos, Mexico
| | - Luis Alberto Manzano-Gómez
- Departamento de Investigación y Desarrollo, 3R Biotec SA de CV, C.P., Tuxtla Gutierrez 29000, Chiapas, Mexico
| | - Adalberto Zenteno-Rojas
- Laboratorio de Ecología Genómica, Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, C.P., Tuxtla Gutierrez 29050, Chiapas, Mexico
| | - Marco Antonio Rogel
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, C.P., Cuernavaca 62210, Morelos, Mexico
| | - Francisco Alexander Rincón-Molina
- Laboratorio de Ecología Genómica, Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, C.P., Tuxtla Gutierrez 29050, Chiapas, Mexico
| | - Víctor Manuel Ruíz-Valdiviezo
- Laboratorio de Ecología Genómica, Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, C.P., Tuxtla Gutierrez 29050, Chiapas, Mexico
| | - Reiner Rincón-Rosales
- Laboratorio de Ecología Genómica, Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, C.P., Tuxtla Gutierrez 29050, Chiapas, Mexico
- Correspondence: ; Tel.: +52-9616150461
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16
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Microbiome: A Tool for Plant Stress Management in Future Production Systems. STRESSES 2022. [DOI: 10.3390/stresses2020014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Climate change, due to the altered composition of the global atmosphere from the “greenhouse effect”, is one of the biggest challenges to agricultural production systems [...]
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17
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Differential Response of Wheat Rhizosphere Bacterial Community to Plant Variety and Fertilization. Int J Mol Sci 2022; 23:ijms23073616. [PMID: 35408978 PMCID: PMC8998456 DOI: 10.3390/ijms23073616] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/17/2022] [Accepted: 03/23/2022] [Indexed: 02/01/2023] Open
Abstract
The taxonomic assemblage and functions of the plant bacterial community are strongly influenced by soil and host plant genotype. Crop breeding, especially after the massive use of nitrogen fertilizers which led to varieties responding better to nitrogen fertilization, has implicitly modified the ability of the plant root to recruit an effective bacterial community. Among the priorities for harnessing the plant bacterial community, plant genotype-by-microbiome interactions are stirring attention. Here, we analyzed the effect of plant variety and fertilization on the rhizosphere bacterial community. In particular, we clarified the presence in the bacterial community of a varietal effect of N and P fertilization treatment. 16S rRNA gene amplicon sequence analysis of rhizospheric soil, collected from four wheat varieties grown under four N-P fertilization regimes, and quantification of functional bacterial genes involved in the nitrogen cycle (nifH; amoA; nirK and nosZ) were performed. Results showed that variety played the most important role and that treatments did not affect either bacterial community diversity or bacterial phyla abundance. Variety-specific response of rhizosphere bacterial community was detected, both in relation to taxa (Nitrospira) and metabolic functions. In particular, the changes related to amino acid and aerobic metabolism and abundance of genes involved in the nitrogen cycle (amoA and nosZ), suggested that plant variety may lead to functional changes in the cycling of the plant-assimilable nitrogen.
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18
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Cangioli L, Vaccaro F, Fini M, Mengoni A, Fagorzi C. Scent of a Symbiont: The Personalized Genetic Relationships of Rhizobium-Plant Interaction. Int J Mol Sci 2022; 23:3358. [PMID: 35328782 PMCID: PMC8954435 DOI: 10.3390/ijms23063358] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 01/24/2023] Open
Abstract
Many molecular signals are exchanged between rhizobia and host legume plants, some of which are crucial for symbiosis to take place, while others are modifiers of the interaction, which have great importance in the competition with the soil microbiota and in the genotype-specific perception of host plants. Here, we review recent findings on strain-specific and host genotype-specific interactions between rhizobia and legumes, discussing the molecular actors (genes, gene products and metabolites) which play a role in the establishment of symbiosis, and highlighting the need for research including the other components of the soil (micro)biota, which could be crucial in developing rational-based strategies for bioinoculants and synthetic communities' assemblage.
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Affiliation(s)
- Lisa Cangioli
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Francesca Vaccaro
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Margherita Fini
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Camilla Fagorzi
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
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19
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Gholizadeh S, Mohammadi SA, Salekdeh GH. Changes in root microbiome during wheat evolution. BMC Microbiol 2022; 22:64. [PMID: 35219318 PMCID: PMC8881823 DOI: 10.1186/s12866-022-02467-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 02/08/2022] [Indexed: 12/20/2022] Open
Abstract
Abstract
Background
Although coevolutionary signatures of host-microbe interactions are considered to engineer the healthy microbiome of humans, little is known about the changes in root-microbiome during plant evolution. To understand how the composition of the wheat and its ancestral species microbiome have changed over the evolutionary processes, we performed a 16S rRNA metagenomic analysis on rhizobacterial communities associated with a phylogenetic framework of four Triticum species T. urartu, T. turgidum, T. durum, and T. aestivum along with their ancestral species Aegilops speltoides, and Ae. tauschii during vegetative and reproductive stages.
Results
In this study, we illustrated that the genome contents of wild species Aegilops speltoides and Ae. tauschii can be significant factors determining the composition of root-associated bacterial communities in domesticated bread wheat. Although it was found that domestication and modern breeding practices might have had a significant impact on microbiome-plant interactions especially at the reproductive stage, we observed an extensive and selective control by wheat genotypes on associated rhizobacterial communities at the same time. Our data also showed a strong genotypic variation within species of T. aestivum and Ae. tauschii, suggesting potential breeding targets for plants surveyed.
Conclusions
This study performed with different genotypes of Triticum and Aegilops species is the first study showing that the genome contents of Ae. speltoides and Ae. tauschii along with domestication-related changes can be significant factors determining the composition of root-associated bacterial communities in bread wheat. It is also indirect evidence that shows a very extensive range of host traits and genes are probably involved in host-microbe interactions. Therefore, understanding the wheat root-associated microbiome needs to take into consideration of its polygenetic mosaic nature.
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20
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Genome analysis of Pseudomonas sp. 14A reveals metabolic capabilities to support epiphytic behavior. World J Microbiol Biotechnol 2022; 38:49. [DOI: 10.1007/s11274-022-03238-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 01/19/2022] [Indexed: 11/26/2022]
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21
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Smulders L, Ferrero V, de la Peña E, Pozo MJ, Díaz Pendón JA, Benítez E, López-García Á. Resistance and Not Plant Fruit Traits Determine Root-Associated Bacterial Community Composition along a Domestication Gradient in Tomato. PLANTS (BASEL, SWITZERLAND) 2021; 11:plants11010043. [PMID: 35009046 PMCID: PMC8747438 DOI: 10.3390/plants11010043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 05/12/2023]
Abstract
Soil bacterial communities are involved in multiple ecosystem services, key in determining plant productivity. Crop domestication and intensive agricultural practices often disrupt species interactions with unknown consequences for rhizosphere microbiomes. This study evaluates whether variation in plant traits along a domestication gradient determines the composition of root-associated bacterial communities; and whether these changes are related to targeted plant traits (e.g., fruit traits) or are side effects of less-often-targeted traits (e.g., resistance) during crop breeding. For this purpose, 18 tomato varieties (wild and modern species) differing in fruit and resistance traits were grown in a field experiment, and their root-associated bacterial communities were characterised. Root-associated bacterial community composition was influenced by plant resistance traits and genotype relatedness. When only considering domesticated tomatoes, the effect of resistance on bacterial OTU composition increases, while the effect due to phylogenetic relatedness decreases. Furthermore, bacterial diversity positively correlated with plant resistance traits. These results suggest that resistance traits not selected during domestication are related to the capacity of tomato varieties to associate with different bacterial groups. Taken together, these results evidence the relationship between plant traits and bacterial communities, pointing out the potential of breeding to affect plant microbiomes.
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Affiliation(s)
- Lisanne Smulders
- Department Enviromental Protection, Estación Experimental del Zaidín (EEZ), CSIC, 18008 Granada, Spain;
- Correspondence:
| | - Victoria Ferrero
- Department of Biodiversity and Environmental Management, Campus de Vegazana s/n, University of León, 24071 León, Spain;
| | - Eduardo de la Peña
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium;
- Department Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ), CSIC, 18008 Granada, Spain; (M.J.P.); (Á.L.-G.)
| | - María J. Pozo
- Department Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ), CSIC, 18008 Granada, Spain; (M.J.P.); (Á.L.-G.)
| | - Juan Antonio Díaz Pendón
- Finca Experimental “La Mayora” CSIC, Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM-UMA-CSIC), 29750 Málaga, Spain;
| | - Emilio Benítez
- Department Enviromental Protection, Estación Experimental del Zaidín (EEZ), CSIC, 18008 Granada, Spain;
| | - Álvaro López-García
- Department Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ), CSIC, 18008 Granada, Spain; (M.J.P.); (Á.L.-G.)
- Department Animal Biology, Plant Biology and Ecology, Universidad de Jaén, 23071 Jaén, Spain
- Instituto Interuniversitario de Investigación del Sistema Tierra en Andalucía (IISTA), 18006 Granada, Spain
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22
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Schaedel M, Hidrobo G, Grossman J. From Microns to Meters: Exploring Advances in Legume Microbiome Diversity for Agroecosystem Benefits. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.668195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Legumes are of primary importance for agroecosystems because they provide protein-rich foods and enhance soil fertility through fixed atmospheric nitrogen. The legume-rhizobia symbiosis that makes this possible has been extensively studied, from basic research on biochemical signaling to practical applications in cropping systems. While rhizobia are the most-studied group of associated microorganisms, the functional benefit they confer to their legume hosts by fixing nitrogen is not performed in isolation. Indeed, non-rhizobia members of the rhizosphere and nodule microbiome are now understood to contribute in multiple ways to nodule formation, legume fitness, and other agroecosystem services. In this review, we summarize advances contributing to our understanding of the diversity and composition of bacterial members of the belowground legume microbiome. We also highlight applied work in legume food and forage crops that link microbial community composition with plant functional benefits. Ultimately, further research will assist in the development of multi-species microbial inoculants and cropping systems that maximize plant nutrient benefits, while reducing sources of agricultural pollution.
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23
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Tomato Domestication Affects Potential Functional Molecular Pathways of Root-Associated Soil Bacteria. PLANTS 2021; 10:plants10091942. [PMID: 34579474 PMCID: PMC8472556 DOI: 10.3390/plants10091942] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/10/2021] [Accepted: 09/14/2021] [Indexed: 01/05/2023]
Abstract
While it has been well evidenced that plant domestication affects the structure of the root-associated microbiome, there is a poor understanding of how domestication-mediated differences between rhizosphere microorganisms functionally affect microbial ecosystem services. In this study, we explore how domestication influenced functional assembly patterns of bacterial communities in the root-associated soil of 27 tomato accessions through a transect of evolution, from plant ancestors to landraces to modern cultivars. Based on molecular analysis, functional profiles were predicted and co-occurrence networks were constructed based on the identification of co-presences of functional units in the tomato root-associated microbiome. The results revealed differences in eight metabolic pathway categories and highlighted the influence of the host genotype on the potential functions of soil bacterial communities. In general, wild tomatoes differed from modern cultivars and tomato landraces which showed similar values, although all ancestral functional characteristics have been conserved across time. We also found that certain functional groups tended to be more evolutionarily conserved in bacterial communities associated with tomato landraces than those of modern varieties. We hypothesize that the capacity of soil bacteria to provide ecosystem services is affected by agronomic practices linked to the domestication process, particularly those related to the preservation of soil organic matter.
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Gastélum G, Rocha J. La milpa como modelo para el estudio de la microbiodiversidad e interacciones planta-bacteria. TIP REVISTA ESPECIALIZADA EN CIENCIAS QUÍMICO-BIOLÓGICAS 2020. [DOI: 10.22201/fesz.23958723e.2020.0.254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
La microbiología agrícola busca reemplazar a los agroquímicos por microorganismos o sus productos como agentes de control biológico, debido a que el uso de tecnologías de la revolución verde tiene efectos negativos sobre el ambiente, los productores y sus familias, los consumidores y la salud de los cultivos. Sin embargo, el conocimiento actual acerca de las interacciones benéficas planta-bacteria en ambientes complejos es limitado e insuficiente, para lograr el éxito esperado de los productos biológicos. Las milpas son agroecosistemas tradicionales donde se cultivan diversas variedades de maíz nativo con otras especies asociadas; no se utiliza riego, ni labranza y aunque su aplicación va en aumento, comúnmente no se utilizan agroquímicos; por esto, la milpa representa una fuente de conocimiento sobre prácticas sustentables. Recientemente, se han descrito cambios en las comunidades microbianas de los sistemas agrícolas a causa de la modernización y a la domesticación de las plantas. En la milpa, también se han identificado interacciones benéficas planta-bacteria que parecen haberse perdido en los cultivos modernos. En esta revisión, discutimos las estrategias clásicas y modernas de la microbiología agrícola que pueden ser aplicadas en el estudio de la milpa. El establecimiento de la milpa como modelo de estudio de las interacciones planta-bacteria puede resultar en la generación del conocimiento necesario para disminuir el uso de agroquímicos en los sistemas agrícolas modernos, así como evitar su creciente uso en las milpas.
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