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Jibril SM, Yan W, Wang Y, Zhu X, Yunying Z, Wu J, Wang L, Zhang L, Li C. Highly diverse microbial community of regenerated seedlings reveals the high capacity of the bulb in lily, Lilium brownii. Front Microbiol 2024; 15:1387870. [PMID: 38903799 PMCID: PMC11188333 DOI: 10.3389/fmicb.2024.1387870] [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: 02/18/2024] [Accepted: 05/15/2024] [Indexed: 06/22/2024] Open
Abstract
Lily bulbs, which have both nutrient storage and reproductive functions, are a representative group of plants for studying the maintenance and transfer of plant-associated microbiomes. In this study, a comparison of the microbial composition of bulbs and their regenerated seedlings cultured under aseptic conditions, as well as subcultured seedlings that succeeded five times, was examined by amplicon sequencing. A total of 62 bacterial taxa and 56 fungal taxa were found to be transferred to the 5th generation in seedlings, which are the core microbiome of lily. After the regeneration of seedlings from bulbs, there was a significant increase in the number of detectable microbial species, and after 1, 3, and 5 successive generations, there was a decrease in the number of detectable species. Interestingly, some "new" microorganisms appeared in each generation of samples; for instance, 167 and 168 bacterial operational taxonomic units (OTUs) in the 3rd and 5th generations of seedlings that were not detected in either bulbs or seedlings of the previous two generations. These results suggest that bulbs can maintain a high diversity of microorganisms, including some with ultra-low abundance, and have a high transfer capacity to tuck shoots through continuous subculture. The diversity and maintenance of the microbiome can provide the necessary microbial reservoir support for regenerating seedlings. This habit of maintaining low abundance and high diversity may be biologically and ecologically critical for maintaining microbiome stability and function due to the sequestration nature of the plant.
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Affiliation(s)
- Sauban Musa Jibril
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Wu Yan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Yi Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Xishen Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Zhou Yunying
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Jie Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Ling Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Limin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Chengyun Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
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Ma Y, Zheng C, Bo Y, Song C, Zhu F. Improving crop salt tolerance through soil legacy effects. FRONTIERS IN PLANT SCIENCE 2024; 15:1396754. [PMID: 38799102 PMCID: PMC11116649 DOI: 10.3389/fpls.2024.1396754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/22/2024] [Indexed: 05/29/2024]
Abstract
Soil salinization poses a critical problem, adversely affecting plant development and sustainable agriculture. Plants can produce soil legacy effects through interactions with the soil environments. Salt tolerance of plants in saline soils is not only determined by their own stress tolerance but is also closely related to soil legacy effects. Creating positive soil legacy effects for crops, thereby alleviating crop salt stress, presents a new perspective for improving soil conditions and increasing productivity in saline farmlands. Firstly, the formation and role of soil legacy effects in natural ecosystems are summarized. Then, the processes by which plants and soil microbial assistance respond to salt stress are outlined, as well as the potential soil legacy effects they may produce. Using this as a foundation, proposed the application of salt tolerance mechanisms related to soil legacy effects in natural ecosystems to saline farmlands production. One aspect involves leveraging the soil legacy effects created by plants to cope with salt stress, including the direct use of halophytes and salt-tolerant crops and the design of cropping patterns with the specific crop functional groups. Another aspect focuses on the utilization of soil legacy effects created synergistically by soil microorganisms. This includes the inoculation of specific strains, functional microbiota, entire soil which legacy with beneficial microorganisms and tolerant substances, as well as the application of novel technologies such as direct use of rhizosphere secretions or microbial transmission mechanisms. These approaches capitalize on the characteristics of beneficial microorganisms to help crops against salinity. Consequently, we concluded that by the screening suitable salt-tolerant crops, the development rational cropping patterns, and the inoculation of safe functional soils, positive soil legacy effects could be created to enhance crop salt tolerance. It could also improve the practical significance of soil legacy effects in the application of saline farmlands.
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Affiliation(s)
- Yue Ma
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chunyan Zheng
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Yukun Bo
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Chunxu Song
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, China
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
- National Observation and Research Station of Agriculture Green Development, Quzhou, China
| | - Feng Zhu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
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Cui C, Li F, Zeng Q, Li C, Shen W, Gao X, Li X, Zhao W, Dong J, Li J, Yang M. Influence of Fertilization Methods and Types on Wheat Rhizosphere Microbiome Community and Functions. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7794-7806. [PMID: 38561246 DOI: 10.1021/acs.jafc.3c09941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
To investigate the effects of fertilization methods and types on wheat rhizosphere microorganisms, macroelement (N, K) and microelement (Zn) fertilizers were applied on wheat by foliar spraying (FS) and root irrigation (RI) methods in a field experiment. The results indicated that fertilization methods and types can have significant impacts on the diversity and structure of rhizospheric microorganisms in wheat. The application method produced more significant effects than the fertilizer type. RI-N played a more important role in improving the wheat yield and quality and affected the changes in some nitrogen-fixing bacterial communities. Finally, eight strains of bacteria belonging to Pseudomonas azotoformans and P. cedrina showed positive effects on the growth of wheat seedlings. Overall, our study provides a better understanding of the dynamics of wheat rhizosphere microbial communities and their relation to fertilization, yield, and quality, showing that plant growth-promoting rhizobacteria with nitrogen fixing may be a potential approach for more sustainable agriculture production.
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Affiliation(s)
- Chao Cui
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, China
| | - Fang Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, China
| | - Quan Zeng
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, China
| | - Chenyang Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, China
| | - Wei Shen
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, China
| | - Xiang Gao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, China
| | - Xiaoyan Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, China
| | - Wanchun Zhao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, China
| | - Jian Dong
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, China
| | - Jiangang Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu 210008, China
| | - Mingming Yang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
- Wheat Engineering Research Center of Shaanxi Province, Yangling 712100, China
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Al Riachy R, Strub C, Durand N, Chochois V, Lopez-Lauri F, Fontana A, Schorr-Galindo S. The Influence of Long-Term Storage on the Epiphytic Microbiome of Postharvest Apples and on Penicillium expansum Occurrence and Patulin Accumulation. Toxins (Basel) 2024; 16:102. [PMID: 38393181 PMCID: PMC10891703 DOI: 10.3390/toxins16020102] [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: 12/21/2023] [Revised: 01/31/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Patulin is a secondary metabolite primarily synthesized by the fungus Penicillium expansum, which is responsible for blue mold disease on apples. The latter are highly susceptible to fungal infection in the postharvest stages. Apples destined to produce compotes are processed throughout the year, which implies that long periods of storage are required under controlled atmospheres. P. expansum is capable of infecting apples throughout the whole process, and patulin can be detected in the end-product. In the present study, 455 apples (organically and conventionally grown), destined to produce compotes, of the variety "Golden Delicious" were sampled at multiple postharvest steps. The apple samples were analyzed for their patulin content and P. expansum was quantified using real-time PCR. The patulin results showed no significant differences between the two cultivation techniques; however, two critical control points were identified: the long-term storage and the deck storage of apples at ambient temperature before transport. Additionally, alterations in the epiphytic microbiota of both fungi and bacteria throughout various steps were investigated through the application of a metabarcoding approach. The alpha and beta diversity analysis highlighted the effect of long-term storage, causing an increase in the bacterial and fungal diversity on apples, and showed significant differences in the microbial communities during the different postharvest steps. The different network analyses demonstrated intra-species relationships. Multiple pairs of fungal and bacterial competitive relationships were observed. Positive interactions were also observed between P. expansum and multiple fungal and bacterial species. These network analyses provide a basis for further fungal and bacterial interaction analyses for fruit disease biocontrol.
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Affiliation(s)
- Reem Al Riachy
- Qualisud, Univ Montpellier, Univ d’Avignon, CIRAD, Institut Agro, IRD, Univ de La Réunion, Montpellier, France; (R.A.R.); (C.S.); (N.D.); (V.C.); (F.L.-L.); (A.F.)
| | - Caroline Strub
- Qualisud, Univ Montpellier, Univ d’Avignon, CIRAD, Institut Agro, IRD, Univ de La Réunion, Montpellier, France; (R.A.R.); (C.S.); (N.D.); (V.C.); (F.L.-L.); (A.F.)
| | - Noël Durand
- Qualisud, Univ Montpellier, Univ d’Avignon, CIRAD, Institut Agro, IRD, Univ de La Réunion, Montpellier, France; (R.A.R.); (C.S.); (N.D.); (V.C.); (F.L.-L.); (A.F.)
- CIRAD, UMR Qualisud, F-34398 Montpellier, France
| | - Vincent Chochois
- Qualisud, Univ Montpellier, Univ d’Avignon, CIRAD, Institut Agro, IRD, Univ de La Réunion, Montpellier, France; (R.A.R.); (C.S.); (N.D.); (V.C.); (F.L.-L.); (A.F.)
- CIRAD, UMR Qualisud, F-34398 Montpellier, France
| | - Félicie Lopez-Lauri
- Qualisud, Univ Montpellier, Univ d’Avignon, CIRAD, Institut Agro, IRD, Univ de La Réunion, Montpellier, France; (R.A.R.); (C.S.); (N.D.); (V.C.); (F.L.-L.); (A.F.)
| | - Angélique Fontana
- Qualisud, Univ Montpellier, Univ d’Avignon, CIRAD, Institut Agro, IRD, Univ de La Réunion, Montpellier, France; (R.A.R.); (C.S.); (N.D.); (V.C.); (F.L.-L.); (A.F.)
| | - Sabine Schorr-Galindo
- Qualisud, Univ Montpellier, Univ d’Avignon, CIRAD, Institut Agro, IRD, Univ de La Réunion, Montpellier, France; (R.A.R.); (C.S.); (N.D.); (V.C.); (F.L.-L.); (A.F.)
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Kumar A, Solanki MK, Wang Z, Solanki AC, Singh VK, Divvela PK. Revealing the seed microbiome: Navigating sequencing tools, microbial assembly, and functions to amplify plant fitness. Microbiol Res 2024; 279:127549. [PMID: 38056172 DOI: 10.1016/j.micres.2023.127549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 12/08/2023]
Abstract
Microbial communities within seeds play a vital role in transmitting themselves to the next generation of plants. These microorganisms significantly impact seed vigor and early seedling growth, for successful crop establishment. Previous studies reported on seed-associated microbial communities and their influence on processes like dormancy release, germination, and disease protection. Modern sequencing and conventional methods reveal microbial community structures and environmental impacts, these information helps in microbial selection and manipulation. These studies form the foundation for using seed microbiomes to enhance crop resilience and productivity. While existing research has primarily focused on characterizing microbiota in dried mature seeds, a significant gap exists in understanding how these microbial communities assemble during seed development. The review also discusses applying seed-associated microorganisms to improve crops in the context of climate change. However, limited knowledge is available about the microbial assembly pattern on seeds, and their impact on plant growth. The review provides insight into microbial composition, functions, and significance for plant health, particularly regarding growth promotion and pest control.
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Affiliation(s)
- Ajay Kumar
- Amity Institute of Biotechnology, Amity University, Sector-125, Noida, Uttar Pradesh 201313, India
| | - Manoj Kumar Solanki
- Department of Life Sciences and Biological Sciences, IES University, Bhopal, Madhya Pradesh, India; Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland.
| | - Zhen Wang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin 537000, China
| | - Anjali Chandrol Solanki
- Department of Agriculture, Mansarover Global University, Bhopal, Madhya Pradesh 462042, India
| | - Vipin Kumar Singh
- Department of Botany, K.S. Saket P.G. College, Ayodhya 224123, Uttar Pradesh, India
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Zeng Q, Zhao Y, Shen W, Han D, Yang M. Seed-to-Seed: Plant Core Vertically Transmitted Microbiota. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19255-19264. [PMID: 38044571 DOI: 10.1021/acs.jafc.3c07092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The plant core microbiota transmitted by seeds have been demonstrated to exist in seeds and adult plants of several crops for multiple generations. They are closely related to plants and are relatively conserved throughout evolution, domestication, and breeding. These microbiota play a vital role in the early stages of plant growth. However, information about their colonization routes, transmission pathways, and final fate remains fragmentary. This review delves into the concept of these microbiota, their colonization sources, transmission pathways, and how they change throughout plant evolution, domestication, and breeding, as well as their effects on plants, based on relevant literature. Finally, the significant potential of incorporating the practical application of seed-transmitted microbiota into plant microbial breeding is emphasized.
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Affiliation(s)
- Quan Zeng
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yang Zhao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei Shen
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dejun Han
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingming Yang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
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Thompson MEH, Shrestha A, Rinne J, Limay-Rios V, Reid L, Raizada MN. The Cultured Microbiome of Pollinated Maize Silks Shifts after Infection with Fusarium graminearum and Varies by Distance from the Site of Pathogen Inoculation. Pathogens 2023; 12:1322. [PMID: 38003787 PMCID: PMC10675081 DOI: 10.3390/pathogens12111322] [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: 10/04/2023] [Revised: 10/31/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Styles transmit pollen-derived sperm nuclei from pollen to ovules, but also transmit environmental pathogens. The microbiomes of styles are likely important for reproduction/disease, yet few studies exist. Whether style microbiome compositions are spatially responsive to pathogens is unknown. The maize pathogen Fusarium graminearum enters developing grain through the style (silk). We hypothesized that F. graminearum treatment shifts the cultured transmitting silk microbiome (TSM) compared to healthy silks in a distance-dependent manner. Another objective of the study was to culture microbes for future application. Bacteria were cultured from husk-covered silks of 14 F. graminearum-treated diverse maize genotypes, proximal (tip) and distal (base) to the F. graminearum inoculation site. Long-read 16S sequences from 398 isolates spanned 35 genera, 71 species, and 238 OTUs. More bacteria were cultured from F. graminearum-inoculated tips (271 isolates) versus base (127 isolates); healthy silks were balanced. F. graminearum caused a collapse in diversity of ~20-25% across multiple taxonomic levels. Some species were cultured exclusively or, more often, from F. graminearum-treated silks (e.g., Delftia acidovorans, Klebsiella aerogenes, K. grimontii, Pantoea ananatis, Stenotrophomonas pavanii). Overall, the results suggest that F. graminearum alters the TSM in a distance-dependent manner. Many isolates matched taxa that were previously identified using V4-MiSeq (core and F. graminearum-induced), but long-read sequencing clarified the taxonomy and uncovered greater diversity than was initially predicted (e.g., within Pantoea). These isolates represent the first comprehensive cultured collection from pathogen-treated maize silks to facilitate biocontrol efforts and microbial marker-assisted breeding.
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Affiliation(s)
- Michelle E. H. Thompson
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.E.H.T.)
| | - Anuja Shrestha
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.E.H.T.)
| | - Jeffrey Rinne
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.E.H.T.)
| | - Victor Limay-Rios
- Department of Plant Agriculture, University of Guelph Ridgetown Campus, 120 Main Street E, Ridgetown, ON N0P 2C0, Canada
| | - Lana Reid
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Central Experimental Farm, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
| | - Manish N. Raizada
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.E.H.T.)
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Moraga D, Latorre K, Muñoz-Torres P, Cárdenas S, Jofré-Quispe A, López-Cepeda J, Bustos L, Balada C, Argaluza MF, González P, Guzmán L. Diversity of Culturable Bacteria from Endemic Medicinal Plants of the Highlands of the Province of Parinacota, Chile. BIOLOGY 2023; 12:920. [PMID: 37508351 PMCID: PMC10376134 DOI: 10.3390/biology12070920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/30/2023]
Abstract
Endemic medicinal plants that grow at altitudes in northern Chile have been traditionally used for therapeutic applications by Aymara doctors. Several studies have analyzed the biological properties of these plants for therapeutic purposes. The aim was to characterize at molecular and biochemical levels the bacteria that live in the rhizosphere and roots from endemic medicinal plants that grow between 3681-5104 m.a.s.l. in the province of Parinacota. Thirty-nine bacteria were isolated from nine medicinal plants under our laboratory conditions. These bacteria were characterized by Gram stain, hydrolase production, plant-growth promotion, anti-fungal and antibacterial activities, and 16S rDNA sequencing. A phylogenetic study revealed the presence of three major phyla, Actinomycetota (46.2%), Bacillota (43.6%), and Pseudomonadota (10.3%). The rhizobacteria strains associated with the Aymara medicinal plant exhibited several interesting biological activities, such as hydrolytic enzymes, plant-growth-promoting traits, and antibacterial and antifungal properties, indicating their potential for developing new bio-based products for agricultural or clinical applications. These results are promising and highlight the need to point toward the search for explanations of the bio-molecular basis of the therapeutic effects of medicinal plants.
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Affiliation(s)
- Daniel Moraga
- Laboratorio de Fisiología, Departamento de Ciencias Biomédicas, Facultad de Medicina, Universidad de Tarapacá, Arica 1000000, Chile
| | - Katina Latorre
- Laboratorio de Microbiología, Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica 1000000, Chile
| | - Patricio Muñoz-Torres
- Laboratorio de Patología Vegetal y Bioproductos, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica 1000000, Chile
| | - Steffany Cárdenas
- Laboratorio de Patología Vegetal y Bioproductos, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica 1000000, Chile
| | - Alan Jofré-Quispe
- Departamento de Ciencias Históricas y Geográficas, Universidad de Tarapacá, Arica 1000000, Chile
| | - José López-Cepeda
- Departamento de Biología, Facultad de Ciencias, Universidad de Tarapacá, Arica 1000000, Chile
| | - Luis Bustos
- Subdepartamento de Gestión de Farmacia, Servicio de Salud Arica, Arica 1000871, Chile
| | - Cristóbal Balada
- Laboratorio de Química Biológica, Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340001, Chile
| | - María Fernanda Argaluza
- Laboratorio de Química Biológica, Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340001, Chile
| | - Pablo González
- Laboratorio de Química Biológica, Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340001, Chile
| | - Leda Guzmán
- Laboratorio de Química Biológica, Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340001, Chile
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Langa-Lomba N, Grimplet J, Sánchez-Hernández E, Martín-Ramos P, Casanova-Gascón J, Julián-Lagunas C, González-García V. Metagenomic Study of Fungal Microbial Communities in Two PDO Somontano Vineyards (Huesca, Spain): Effects of Age, Plant Genotype, and Initial Phytosanitary Status on the Priming and Selection of their Associated Microorganisms. PLANTS (BASEL, SWITZERLAND) 2023; 12:2251. [PMID: 37375877 DOI: 10.3390/plants12122251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 05/29/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023]
Abstract
The study of microbial communities associated with different plants of agronomic interest has allowed, in recent years, to answer a number of questions related to the role and influence of certain microbes in key aspects of their autoecology, such as improving the adaptability of the plant host to different abiotic or biotic stresses. In this study, we present the results of the characterization, through both high-throughput sequencing and classical microbiological methods, of the fungal microbial communities associated with grapevine plants in two vineyards of different ages and plant genotypes located in the same biogeographical unit. The study is configured as an approximation to the empirical demonstration of the concept of "microbial priming" by analyzing the alpha- and beta-diversity present in plants from two plots subjected to the same bioclimatic regime to detect differences in the structure and taxonomic composition of the populations. The results were compared with the inventories of fungal diversity obtained by culture-dependent methods to establish, where appropriate, correlations between both microbial communities. Metagenomic data showed a differential enrichment of the microbial communities in the two vineyards studied, including the populations of plant pathogens. This is tentatively explained due to factors such as the different time of exposure to microbial infection, different plant genotype, and different starting phytosanitary situation. Thus, results suggest that each plant genotype recruits differential fungal communities and presents different profiles of associated potential microbial antagonists or communities of pathogenic species.
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Affiliation(s)
- Natalia Langa-Lomba
- Instituto Universitario de Investigación en Ciencias Ambientales de Aragón (IUCA), EPS, University of Zaragoza, Carretera de Cuarte s/n, 22071 Huesca, Spain
- Departamento de Sistemas Agrícolas, Forestales y Medio Ambiente, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda. Montañana 930, 50059 Zaragoza, Spain
| | - Jerome Grimplet
- Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), 50059 Zaragoza, Spain
- Departamento de Ciencia Vegetal, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda. Montañana 930, 50059 Zaragoza, Spain
| | - Eva Sánchez-Hernández
- Department of Agricultural and Forestry Engineering, ETSIIAA, Universidad de Valladolid, Avenida de Madrid 44, 34004 Palencia, Spain
| | - Pablo Martín-Ramos
- Department of Agricultural and Forestry Engineering, ETSIIAA, Universidad de Valladolid, Avenida de Madrid 44, 34004 Palencia, Spain
| | - José Casanova-Gascón
- Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), EPS, University of Zaragoza, Carretera de Cuarte s/n, 22071 Huesca, Spain
| | - Carmen Julián-Lagunas
- Departamento de Sistemas Agrícolas, Forestales y Medio Ambiente, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda. Montañana 930, 50059 Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), 50059 Zaragoza, Spain
| | - Vicente González-García
- Departamento de Sistemas Agrícolas, Forestales y Medio Ambiente, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda. Montañana 930, 50059 Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), 50059 Zaragoza, Spain
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10
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Munir R, Jan M, Muhammad S, Afzal M, Jan N, Yasin MU, Munir I, Iqbal A, Yang S, Zhou W, Gan Y. Detrimental effects of Cd and temperature on rice and functions of microbial community in paddy soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 324:121371. [PMID: 36878274 DOI: 10.1016/j.envpol.2023.121371] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/30/2023] [Accepted: 02/26/2023] [Indexed: 06/18/2023]
Abstract
Heavy metal (HM) contamination and high environmental temperature (HT) are caused by anthropogenic activities that negatively impact soil microbial communities and agricultural productivity. Although HM contaminations have deleterious effects on microbes and plants; there are hardly any reports on the combined effects of HM and HT. Here, we reported that HT coupled with cadmium (Cd) accumulation in soil and irrigated water could seriously affect crop growth and productivity, alternatively influencing the microbial community and nutrient cycles of paddy soils in rice fields. We analyzed different mechanisms of plants and microflora in the rhizospheric region, such as plant rhizospheric nitrification, endophytes colonization, nutrient uptake, and physiology of temperature-sensitive (IR64) and temperature-resistant Huanghuazhan (HZ) rice cultivars against different Cd levels (2, 5 and 10 mg kg-1) with rice plants grown under 25 °C and 40 °C temperatures. Consequently, an increment in Cd accumulation was observed with rising temperature leading to enhanced expression of OsNTRs. In contrast, a greater decline in the microbial community was detected in IR64 cultivar than HZ. Similarly, ammonium oxidation, root-IAA, shoot-ABA production, and 16S rRNA gene abundance in the rhizosphere and endosphere were significantly influenced by HT and Cd levels, resulting in a significant decrease in the colonization of endophytes and the surface area of roots, leading to a decreased N uptake from the soil. Overall, the outcomes of this study unveiled the novel effects of Cd, temperature, and their combined effect on rice growth and functions of the microbial community. These results provide effective strategies to overcome Cd-phytotoxicity on the health of endophytes and rhizospheric bacteria in Cd-contaminated soil by using temperature-tolerant rice cultivars.
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Affiliation(s)
- Raheel Munir
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Mehmood Jan
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Sajid Muhammad
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Muhammad Afzal
- Institute of Soil and Water Resources and Environmental Science, College of Environment and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Nazia Jan
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Muhammad Umair Yasin
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Iqbal Munir
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, 25130, Pakistan
| | - Aqib Iqbal
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, 25130, Pakistan
| | - Shuaiqi Yang
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Weijun Zhou
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yinbo Gan
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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11
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Ramirez-Villacis DX, Erazo-Garcia P, Quijia-Pillajo J, Llerena-Llerena S, Barriga-Medina N, Jones CD, Leon-Reyes A. Influence of Grafting on Rootstock Rhizosphere Microbiome Assembly in Rosa sp. 'Natal Brier'. BIOLOGY 2023; 12:biology12050663. [PMID: 37237477 DOI: 10.3390/biology12050663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/18/2023] [Accepted: 04/18/2023] [Indexed: 05/28/2023]
Abstract
The root microbiome is vital in plant development and health and is highly influenced by crop cultural practices. Rose (Rosa sp.) is the most popular cut flower worldwide. Grafting in rose production is a standard practice to increase yield, improve flower quality, or reduce root-associated pests and diseases. 'Natal Brier' is a standard rootstock used in most commercial operations in Ecuador and Colombia, leading countries in producing and exporting ornamentals. It is known that the rose scion genotype affects root biomass and the root exudate profile of grafted plants. However, little is known about the influence of the rose scion genotype on the rhizosphere microbiome. We examined the influence of grafting and scion genotype on the rhizosphere microbiome of the rootstock 'Natal Brier'. The microbiomes of the non-grafted rootstock and the rootstock grafted with two red rose cultivars were assessed using 16S rRNA and ITS sequencing. Grafting changed microbial community structure and function. Further, analysis of grafted plant samples revealed that the scion genotype highly influences the rootstock microbiome. Under the presented experimental conditions, the rootstock 'Natal Brier' core microbiome consisted of 16 bacterial and 40 fungal taxa. Our results highlight that the scion genotype influences root microbe's recruitment, which might also influence the functionality of assembled microbiomes.
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Affiliation(s)
- Dario X Ramirez-Villacis
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito 170109, Ecuador
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Pablo Erazo-Garcia
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito 170109, Ecuador
| | - Juan Quijia-Pillajo
- Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH 43210, USA
| | - Sol Llerena-Llerena
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito 170109, Ecuador
| | - Noelia Barriga-Medina
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito 170109, Ecuador
| | - Corbin D Jones
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Antonio Leon-Reyes
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito 170109, Ecuador
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
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12
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Yang S, Liu H, Xie P, Wen T, Shen Q, Yuan J. Emerging Pathways for Engineering the Rhizosphere Microbiome for Optimal Plant Health. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4441-4449. [PMID: 36890647 DOI: 10.1021/acs.jafc.2c08758] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The increasing impacts of global climate change on crop performance pose a significant threat to global food security. The rhizosphere microbiomes intimately interact with the plant and can largely facilitate plants in growth promotion and stress resistance via multiple mechanisms. This review focuses on approaches for harnessing the rhizosphere microbiomes to produce beneficial effects toward enhanced crop productivity, including the use of organic and inorganic amendments, and microbial inoculants. Emerging methods, such as the utilization of synthetic microbial consortia, host-mediated microbiome engineering, prebiotics made from specific plant root exudates, and crop breeding to promote beneficial plant-microbiome interactions, are highlighted. Updating our knowledge in this field is critical for understanding and improving plant-microbiome interactions, thereby enhancing plant adaptiveness to changing environmental conditions.
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Affiliation(s)
- Shengdie Yang
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2753, Australia
| | - Penghao Xie
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Tao Wen
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Yuan
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
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13
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Seasonal activities of the phyllosphere microbiome of perennial crops. Nat Commun 2023; 14:1039. [PMID: 36823152 PMCID: PMC9950430 DOI: 10.1038/s41467-023-36515-y] [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: 11/08/2022] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
Understanding the interactions between plants and microorganisms can inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on replicated plots of field-grown switchgrass and miscanthus, and to quantify their activities over two growing seasons for switchgrass. We use metagenome and metatranscriptome sequencing and curate 40 medium- and high-quality metagenome-assembled-genomes (MAGs). We find that classes represented by these MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) are active in the late season, and upregulate transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase. Stress-associated pathways are expressed for most MAGs, suggesting engagement with the host environment. We also detect seasonally activated biosynthetic pathways for terpenes and various non-ribosomal peptide pathways that are poorly annotated. Our findings support that leaf-associated bacterial populations are seasonally dynamic and responsive to host cues.
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14
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Wang YZ, Zhou SYD, Zhou XY, An XL, Su JQ. Manure and biochar have limited effect on lettuce leaf endophyte resistome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160515. [PMID: 36442632 DOI: 10.1016/j.scitotenv.2022.160515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 11/04/2022] [Accepted: 11/22/2022] [Indexed: 06/16/2023]
Abstract
Soil amendment with manure compost and biochar is widely adopted to improve soil fertility and promote plant growth, and their effects on soil microbial communities and resistome have been well documented. However, there is sparse information regarding their effects on vegetable endophytes, which represent a major source of human exposure to pathogens and antibiotic resistance genes (ARGs) when eaten raw. Here, we investigated the impacts of manure compost or biochar addition on the bacterial community compositions and ARGs in the soil-lettuce continuum including soil, seed, leaf, and root samples. A total of 137 ARGs and 31 mobile genetic elements (MGEs) were detected in all the samples after 60 days of cultivation. The relative abundance of ARGs and the diversity of bacteria communities presented a consistent decreasing trend from soil to root endophytes, then leaf endophytes. Manure compost addition increased the diversity and abundance of ARGs in soil, while significant changes in the ARG profiles and bacterial communities were not observed in leaf endophytes after manure compost or biochar addition, or both. Bipartite networks analysis suggested that seed microbiome was one of the major sources of plant endophytes and ARGs. Twenty potential human pathogens were isolated from lettuce, indicating potential exposure risk to pathogens via the consumption of raw lettuce. These results suggest limited impacts of manure compost and biochar addition on lettuce endophytes and highlight the contribution of seed microbiome to endophyte ARG profiles.
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Affiliation(s)
- Yan-Zi Wang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shu-Yi-Dan Zhou
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Xin-Yuan Zhou
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin-Li An
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China.
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China.
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15
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Li G, Liu P, Zhao J, Su L, Zhao M, Jiang Z, Zhao Y, Yang X. Correlation of microbiomes in "plant-insect-soil" ecosystem. Front Microbiol 2023; 14:1088532. [PMID: 36793880 PMCID: PMC9922863 DOI: 10.3389/fmicb.2023.1088532] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/03/2023] [Indexed: 02/03/2023] Open
Abstract
Introduction Traditional chemical control methods pose a damaging effect on farmland ecology, and their long-term use has led to the development of pest resistance. Methods Here, we analyzed the correlations and differences in the microbiome present in the plant and soil of sugarcane cultivars exhibiting different insect resistance to investigate the role played by microbiome in crop insect resistance. We evaluated the microbiome of stems, topsoil, rhizosphere soil, and striped borers obtained from infested stems, as well as soil chemical parameters. Results and Discussion Results showed that microbiome diversity was higher in stems of insect-resistant plants, and contrast, lower in the soil of resistant plants, with fungi being more pronounced than bacteria. The microbiome in plant stems was almost entirely derived from the soil. The microbiome of insect-susceptible plants and surrounding soil tended to change towards that of insect-resistant plants after insect damage. Insects' microbiome was mainly derived from plant stems and partly from the soil. Available potassium showed an extremely significant correlation with soil microbiome. This study validated the role played by the microbiome ecology of plant-soil-insect system in insect resistance and provided a pre-theoretical basis for crop resistance control.
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Affiliation(s)
- Guomeng Li
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Peng Liu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Jihan Zhao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Liangyinan Su
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Mengyu Zhao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Zhengjie Jiang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Yang Zhao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China,*Correspondence: Yang Zhao,
| | - Xiping Yang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China,Xiping Yang,
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16
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Wolfgang A, Temme N, Tilcher R, Berg G. Understanding the sugar beet holobiont for sustainable agriculture. Front Microbiol 2023; 14:1151052. [PMID: 37138624 PMCID: PMC10149816 DOI: 10.3389/fmicb.2023.1151052] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/31/2023] [Indexed: 05/05/2023] Open
Abstract
The importance of crop-associated microbiomes for the health and field performance of plants has been demonstrated in the last decades. Sugar beet is the most important source of sucrose in temperate climates, and-as a root crop-yield heavily depends on genetics as well as on the soil and rhizosphere microbiomes. Bacteria, fungi, and archaea are found in all organs and life stages of the plant, and research on sugar beet microbiomes contributed to our understanding of the plant microbiome in general, especially of microbiome-based control strategies against phytopathogens. Attempts to make sugar beet cultivation more sustainable are increasing, raising the interest in biocontrol of plant pathogens and pests, biofertilization and -stimulation as well as microbiome-assisted breeding. This review first summarizes already achieved results on sugar beet-associated microbiomes and their unique traits, correlating to their physical, chemical, and biological peculiarities. Temporal and spatial microbiome dynamics during sugar beet ontogenesis are discussed, emphasizing the rhizosphere formation and highlighting knowledge gaps. Secondly, potential or already tested biocontrol agents and application strategies are discussed, providing an overview of how microbiome-based sugar beet farming could be performed in the future. Thus, this review is intended as a reference and baseline for further sugar beet-microbiome research, aiming to promote investigations in rhizosphere modulation-based biocontrol options.
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Affiliation(s)
- Adrian Wolfgang
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Nora Temme
- KWS SAAT SE & Co. KGaA, Einbeck, Germany
| | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Microbiome Biotechnology Department, Leibniz-Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- *Correspondence: Gabriele Berg
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17
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Nataraja KN, Dhanyalakshmi KH, Govind G, Oelmüller R. Activation of drought tolerant traits in crops: endophytes as elicitors. PLANT SIGNALING & BEHAVIOR 2022; 17:2120300. [PMID: 36373371 PMCID: PMC9665085 DOI: 10.1080/15592324.2022.2120300] [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: 06/07/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
Drought challenges crop production worldwide. The issue is aggravated by frequent drought episodes and unpredictable rainfall patterns associated with global climate change. While the efforts to breed drought-resistant crop varieties are progressing, the need of the hour is immediate strategies to sustain the yields of existing ones. As per recent studies, stress adaptive traits can be activated using specific elicitors. Endophytes that inhabit host plants asymptomatically are natural elicitors/bio-stimulators capable of activating host gene expression, conferring several benefits to the hosts. This review discusses the scope of using trait-specific endophytes in activating drought adaptive traits in crop varieties.
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Affiliation(s)
- Karaba N Nataraja
- Plant Molecular Biology Laboratory, Department of Crop Physiology, University of Agricultural Sciences Bangalore (UASB), GKVK Bengaluru, India
| | - KH Dhanyalakshmi
- Department of Plant Physiology, Regional Agricultural Research Station Pattambi, Kerala Agricultural University, Thrissur, Kerala, India
| | - Geetha Govind
- Department of Biotechnology, College of Agriculture, UASB, Hassan, India
| | - Ralf Oelmüller
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular, Botany, Friedrich-Schiller-University Jena, Jena, Germany
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18
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Liang D, Bowatte S. Seed endophytic ammonia oxidizing bacteria in Elymus nutans transmit to offspring plants and contribute to nitrification in the root zone. Front Microbiol 2022; 13:1036897. [PMID: 36523826 PMCID: PMC9744808 DOI: 10.3389/fmicb.2022.1036897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/14/2022] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Ammonia oxidizing bacteria (AOB) in soil are of great biological importance as they regulate the cycling of N in agroecosystems. Plants are known to harbor AOB but how they occupy the plant is an unresolved question. METHODS Metabarcoding studies were carried out using Illumina MiSeq sequencing to test the potential of seed vectored AOB exchange between plants and soil. RESULTS AND DISCUSSION We found 27 sequences associated with AOB strains belonging to the genera Nitrosospira, Nitrosovibrio, and Nitrosomonas inhabiting Elymus nutans seeds collected from four geographically distanced alpine meadows. Nitrosospira multiformis was the most dominant across the four locations. The AOB community in E. nutans seeds was compared with that of the leaves, roots and soil in one location. Soil and seeds harbored a rich but dissimilar AOB community, and Nitrosospira sp. PJA1, Nitrosospira sp. Nsp17 and Nitrosovibrio sp. RY3C were present in all plant parts and soils. When E. nutans seeds were germinated in sterilized growth medium under greenhouse conditions, the AOB in seeds later appeared in leaves, roots and growth medium, and contributed to nitrification. Testing the AOB community of the second-generation seeds confirmed vertical transmission, but low richness was observed. CONCLUSION These results suggest seed vectored AOB may play a critical role in N cycle.
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Affiliation(s)
- Danni Liang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Saman Bowatte
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
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19
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Gutierrez A, Grillo MA. Effects of Domestication on Plant-Microbiome Interactions. PLANT & CELL PHYSIOLOGY 2022; 63:1654-1666. [PMID: 35876043 DOI: 10.1093/pcp/pcac108] [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: 02/02/2022] [Revised: 07/15/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Through the process of domestication, selection is targeted on a limited number of plant traits that are typically associated with yield. As an unintended consequence, domesticated plants often perform poorly compared to their wild progenitors for a multitude of traits that were not under selection during domestication, including abiotic and biotic stress tolerance. Over the past decade, advances in sequencing technology have allowed for the rigorous characterization of host-associated microbial communities, termed the microbiome. It is now clear that nearly every conceivable plant interaction with the environment is mediated by interactions with the microbiome. For this reason, plant-microbiome interactions are an area of great promise for plant breeding and crop improvement. Here, we review the literature to assess the potential impact that domestication has had on plant-microbiome interactions and the current understanding of the genetic basis of microbiome variation to inform plant breeding efforts. Overall, we find limited evidence that domestication impacts the diversity of microbiomes, but domestication is often associated with shifts in the abundance and composition of microbial communities, including taxa of known functional significance. Moreover, genome-wide association studies and mutant analysis have not revealed a consistent set of core candidate genes or genetic pathways that confer variation in microbiomes across systems. However, such studies do implicate a consistent role for plant immunity, root traits, root and leaf exudates and cell wall integrity as key traits that control microbiome colonization and assembly. Therefore, selection on these key traits may pose the most immediate promise for enhancing plant-microbiome interactions through breeding.
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Affiliation(s)
- Andres Gutierrez
- Department of Biology, Loyola University Chicago, 1032 W. Sheridan Rd, Chicago, IL 60660, USA
| | - Michael A Grillo
- Department of Biology, Loyola University Chicago, 1032 W. Sheridan Rd, Chicago, IL 60660, USA
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20
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Obermeier C, Mason AS, Meiners T, Petschenka G, Rostás M, Will T, Wittkop B, Austel N. Perspectives for integrated insect pest protection in oilseed rape breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3917-3946. [PMID: 35294574 PMCID: PMC9729155 DOI: 10.1007/s00122-022-04074-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/01/2022] [Indexed: 05/02/2023]
Abstract
In the past, breeding for incorporation of insect pest resistance or tolerance into cultivars for use in integrated pest management schemes in oilseed rape/canola (Brassica napus) production has hardly ever been approached. This has been largely due to the broad availability of insecticides and the complexity of dealing with high-throughput phenotyping of insect performance and plant damage parameters. However, recent changes in the political framework in many countries demand future sustainable crop protection which makes breeding approaches for crop protection as a measure for pest insect control attractive again. At the same time, new camera-based tracking technologies, new knowledge-based genomic technologies and new scientific insights into the ecology of insect-Brassica interactions are becoming available. Here we discuss and prioritise promising breeding strategies and direct and indirect breeding targets, and their time-perspective for future realisation in integrated insect pest protection of oilseed rape. In conclusion, researchers and oilseed rape breeders can nowadays benefit from an array of new technologies which in combination will accelerate the development of improved oilseed rape cultivars with multiple insect pest resistances/tolerances in the near future.
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Affiliation(s)
- Christian Obermeier
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - Annaliese S Mason
- Plant Breeding Department, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Torsten Meiners
- Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Julius Kühn Institute, Koenigin-Luise-Str. 19, 14195, Berlin, Germany
| | - Georg Petschenka
- Department of Applied Entomology, University of Hohenheim, Otto-Sander-Straße 5, 70599, Stuttgart, Germany
| | - Michael Rostás
- Division of Agricultural Entomology, University of Göttingen, Grisebachstr. 6, 37077, Göttingen, Germany
| | - Torsten Will
- Insitute for Resistance Research and Stress Tolerance, Julius Kühn Insitute, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Benjamin Wittkop
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Nadine Austel
- Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Julius Kühn Institute, Koenigin-Luise-Str. 19, 14195, Berlin, Germany
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21
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Li K, Cheng K, Wang H, Zhang Q, Yang Y, Jin Y, He X, Wu R. Disentangling leaf-microbiome interactions in Arabidopsis thaliana by network mapping. FRONTIERS IN PLANT SCIENCE 2022; 13:996121. [PMID: 36275601 PMCID: PMC9583167 DOI: 10.3389/fpls.2022.996121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
The leaf microbiota plays a key role in plant development, but a detailed mechanism of microbe-plant relationships remains elusive. Many genome-wide association studies (GWAS) have begun to map leaf microbes, but few have systematically characterized the genetics of how microbes act and interact. Previously, we integrated behavioral ecology and game theory to define four types of microbial interactions - mutualism, antagonism, aggression, and altruism, in a microbial community assembly. Here, we apply network mapping to identify specific plant genes that mediate the topological architecture of microbial networks. Analyzing leaf microbiome data from an Arabidopsis GWAS, we identify several heritable hub microbes for leaf microbial communities and detect 140-728 SNPs (Single nucleotide polymorphisms) responsible for emergent properties of microbial network. We reconstruct Bayesian genetic networks from which to identify 22-43 hub genes found to code molecular pathways related to leaf growth, abiotic stress responses, disease resistance and nutrition uptake. A further path analysis visualizes how genetic variants of Arabidopsis affect its fecundity through the internal workings of the leaf microbiome. We find that microbial networks and their genetic control vary along spatiotemporal gradients. Our study provides a new avenue to reveal the "endophenotype" role of microbial networks in linking genotype to end-point phenotypes in plants. Our integrative theory model provides a powerful tool to understand the mechanistic basis of structural-functional relationships within the leaf microbiome and supports the need for future research on plant breeding and synthetic microbial consortia with a specific function.
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Affiliation(s)
- Kaihang Li
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kexin Cheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Haochen Wang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Qi Zhang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yan Yang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yi Jin
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiaoqing He
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, China
| | - Rongling Wu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, China
- Departments of Public Health Sciences and Statistics, Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, United States
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22
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Pradhan S, Tyagi R, Sharma S. Combating biotic stresses in plants by synthetic microbial communities: Principles, applications, and challenges. J Appl Microbiol 2022; 133:2742-2759. [PMID: 36039728 DOI: 10.1111/jam.15799] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022]
Abstract
Presently, agriculture worldwide is facing the major challenge of feeding the increasing population sustainably. The conventional practices have not only failed to meet the projected needs, but also led to tremendous environmental consequences. Hence, to ensure a food-secure and environmentally sound future, the major thrust is on sustainable alternatives. Due to challenges associated with conventional means of application of biocontrol agents in the management of biotic stresses in agro-ecosystems, significant transformations in this context is needed. The crucial role played by soil microbiomes in efficiently and sustainably managing the agricultural production has unfolded a newer approach of rhizospheric engineering that shows immense promise in mitigating biotic stresses in an eco-friendly manner. The strategy of generating synthetic microbial communities (SynCom), by integrating omics approaches with traditional techniques of enumeration and in-depth analysis of plant-microbe interactions, is encouraging. The review discusses the significance of the rhizospheric microbiome in plant's fitness, and its manipulation for enhancing plant attributes. The focus of the review is to critically analyze the potential tools for the design and utilization of SynCom as a sustainable approach for rhizospheric engineering to ameliorate biotic stresses in plants. Further, based on the synthesis of reports in the area, we have put forth possible solutions to some of the critical issues that impair the large-scale application of SynComs in agriculture.
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Affiliation(s)
- Salila Pradhan
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi
| | - Rashi Tyagi
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi
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23
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Broccanello C, Ravi S, Deb S, Bolton M, Secor G, Richards C, Maretto L, Lucia MCD, Bertoldo G, Orsini E, Ronquillo-López MG, Concheri G, Campagna G, Squartini A, Stevanato P. Bacterial endophytes as indicators of susceptibility to Cercospora Leaf Spot (CLS) disease in Beta vulgaris L. Sci Rep 2022; 12:10719. [PMID: 35739218 PMCID: PMC9226160 DOI: 10.1038/s41598-022-14769-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 06/13/2022] [Indexed: 12/03/2022] Open
Abstract
The fungus Cercospora beticola causes Cercospora Leaf Spot (CLS) of sugar beet (Beta vulgaris L.). Despite the global importance of this disease, durable resistance to CLS has still not been obtained. Therefore, the breeding of tolerant hybrids is a major goal for the sugar beet sector. Although recent studies have suggested that the leaf microbiome composition can offer useful predictors to assist plant breeders, this is an untapped resource in sugar beet breeding efforts. Using Ion GeneStudio S5 technology to sequence amplicons from seven 16S rRNA hypervariable regions, the most recurring endophytes discriminating CLS-symptomatic and symptomless sea beets (Beta vulgaris L.ssp. maritima) were identified. This allowed the design of taxon-specific primer pairs to quantify the abundance of the most representative endophytic species in large naturally occurring populations of sea beet and subsequently in sugar beet breeding genotypes under either CLS symptomless or infection stages using qPCR. Among the screened bacterial genera, Methylobacterium and Mucilaginibacter were found to be significantly (p < 0.05) more abundant in symptomatic sea beets with respect to symptomless. In cultivated sugar beet material under CLS infection, the comparison between resistant and susceptible genotypes confirmed that the susceptible genotypes hosted higher contents of the above-mentioned bacterial genera. These results suggest that the abundance of these species can be correlated with increased sensitivity to CLS disease. This evidence can further prompt novel protocols to assist plant breeding of sugar beet in the pursuit of improved pathogen resistance.
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Affiliation(s)
- Chiara Broccanello
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Viale Dell'Università, Legnaro, PD, Italy
| | - Samathmika Ravi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Viale Dell'Università, Legnaro, PD, Italy
| | - Saptarathi Deb
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Viale Dell'Università, Legnaro, PD, Italy
| | - Melvin Bolton
- Northern Crop Science Laboratory, U.S. Dept. Agriculture, Fargo, ND, USA
| | - Gary Secor
- Plant Pathology Department, North Dakota State University, Fargo, ND, USA
| | | | - Laura Maretto
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Viale Dell'Università, Legnaro, PD, Italy
| | - Maria Cristina Della Lucia
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Viale Dell'Università, Legnaro, PD, Italy
| | - Giovanni Bertoldo
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Viale Dell'Università, Legnaro, PD, Italy
| | - Elena Orsini
- Strube Research GmbH & Co. KG, Söllingen, Germany
| | | | - Giuseppe Concheri
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Viale Dell'Università, Legnaro, PD, Italy
| | | | - Andrea Squartini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Viale Dell'Università, Legnaro, PD, Italy
| | - Piergiorgio Stevanato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padua, Viale Dell'Università, Legnaro, PD, Italy.
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24
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Oyserman BO, Flores SS, Griffioen T, Pan X, van der Wijk E, Pronk L, Lokhorst W, Nurfikari A, Paulson JN, Movassagh M, Stopnisek N, Kupczok A, Cordovez V, Carrión VJ, Ligterink W, Snoek BL, Medema MH, Raaijmakers JM. Disentangling the genetic basis of rhizosphere microbiome assembly in tomato. Nat Commun 2022; 13:3228. [PMID: 35710629 PMCID: PMC9203511 DOI: 10.1038/s41467-022-30849-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/19/2022] [Indexed: 12/31/2022] Open
Abstract
Microbiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, we map the molecular features of the rhizosphere microbiome as quantitative traits of a diverse hybrid population of wild and domesticated tomato. Gene content analysis of prioritized tomato quantitative trait loci suggests a genetic basis for differential recruitment of various rhizobacterial lineages, including a Streptomyces-associated 6.31 Mbp region harboring tomato domestication sweeps and encoding, among others, the iron regulator FIT and the water channel aquaporin SlTIP2.3. Within metagenome-assembled genomes of root-associated Streptomyces and Cellvibrio, we identify bacterial genes involved in metabolism of plant polysaccharides, iron, sulfur, trehalose, and vitamins, whose genetic variation associates with specific tomato QTLs. By integrating 'microbiomics' and quantitative plant genetics, we pinpoint putative plant and reciprocal rhizobacterial traits underlying microbiome assembly, thereby providing a first step towards plant-microbiome breeding programs.
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Affiliation(s)
- Ben O Oyserman
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
| | - Stalin Sarango Flores
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Thom Griffioen
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Xinya Pan
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Elmar van der Wijk
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Lotte Pronk
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Wouter Lokhorst
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Azkia Nurfikari
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Joseph N Paulson
- Department of Data Sciences, Genentech, Inc. South San Francisco, South San Francisco, CA, USA
| | - Mercedeh Movassagh
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Data Sciences Dana Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Nejc Stopnisek
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Anne Kupczok
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Wilco Ligterink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.
- Institute of Biology, Leiden University, Leiden, The Netherlands.
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25
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Tao S, Zhang Y, Tian C, Duplessis S, Zhang N. Elevated Ozone Concentration and Nitrogen Addition Increase Poplar Rust Severity by Shifting the Phyllosphere Microbial Community. J Fungi (Basel) 2022; 8:jof8050523. [PMID: 35628778 PMCID: PMC9148057 DOI: 10.3390/jof8050523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/16/2022] [Accepted: 05/16/2022] [Indexed: 12/04/2022] Open
Abstract
Tropospheric ozone and nitrogen deposition are two major environmental pollutants. A great deal of research has focused on the negative impacts of elevated O3 and the complementary effect of soil N addition on the physiological properties of trees. However, it has been overlooked how elevated O3 and N addition affect tree immunity in face of pathogen infection, as well as of the important roles of phyllosphere microbiome community in host–pathogen–environment interplay. Here, we examined the effects of elevated O3 and soil N addition on poplar leaf rust [Melampsora larici-populina] severity of two susceptible hybrid poplars [clone ‘107’: Populus euramericana cv. ‘74/76’; clone ‘546’: P. deltoides Í P. cathayana] in Free-Air-Controlled-Environment plots, in addition, the link between Mlp-susceptibility and changes in microbial community was determined using Miseq amplicon sequencing. Rust severity of clone ‘107’ significantly increased under elevated O3 or N addition only; however, the negative impact of elevated O3 could be significantly mitigated when accompanied by N addition, likewise, this trade-off was reflected in its phyllosphere microbial α-diversity responding to elevated O3 and N addition. However, rust severity of clone ‘546’ did not differ significantly in the cases of elevated O3 and N addition. Mlp infection altered microbial community composition and increased its sensitivity to elevated O3, as determined by the markedly different abundance of taxa. Elevated O3 and N addition reduced the complexity of microbial community, which may explain the increased severity of poplar rust. These findings suggest that poplars require a changing phyllosphere microbial associations to optimize plant immunity in response to environmental changes.
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Affiliation(s)
- Siqi Tao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China; (S.T.); (Y.Z.); (C.T.)
| | - Yunxia Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China; (S.T.); (Y.Z.); (C.T.)
| | - Chengming Tian
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China; (S.T.); (Y.Z.); (C.T.)
| | | | - Naili Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China; (S.T.); (Y.Z.); (C.T.)
- Correspondence:
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26
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Kang S, Kim KT, Choi J, Kim H, Cheong K, Bandara A, Lee YH. Genomics and Informatics, Conjoined Tools Vital for Understanding and Protecting Plant Health. PHYTOPATHOLOGY 2022; 112:981-995. [PMID: 34889667 DOI: 10.1094/phyto-10-21-0418-rvw] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Genomics' impact on crop production continuously expands. The number of sequenced plant and microbial species and strains representing diverse populations of individual species rapidly increases thanks to the advent of next-generation sequencing technologies. Their genomic blueprints revealed candidate genes involved in various functions and processes crucial for crop health and helped in understanding how the sequenced organisms have evolved at the genome level. Functional genomics quickly translates these blueprints into a detailed mechanistic understanding of how such functions and processes work and are regulated; this understanding guides and empowers efforts to protect crops from diverse biotic and abiotic threats. Metagenome analyses help identify candidate microbes crucial for crop health and uncover how microbial communities associated with crop production respond to environmental conditions and cultural practices, presenting opportunities to enhance crop health by judiciously configuring microbial communities. Efficient conversion of disparate types of massive genomics data into actionable knowledge requires a robust informatics infrastructure supporting data preservation, analysis, and sharing. This review starts with an overview of how genomics came about and has quickly transformed life science. We illuminate how genomics and informatics can be applied to investigate various crop health-related problems using selected studies. We end the review by noting why community empowerment via crowdsourcing is crucial to harnessing genomics to protect global food and nutrition security without continuously expanding the environmental footprint of crop production.
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Affiliation(s)
- Seogchan Kang
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Ki-Tae Kim
- Department of Agricultural Life Science, Sunchon National University, Suncheon 57922, Korea
| | - Jaeyoung Choi
- Korea Institute of Science and Technology Gangneung Institute of Natural Products, Gangneung 25451, Korea
| | - Hyun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Kyeongchae Cheong
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Korea
| | - Ananda Bandara
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Korea
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27
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El‐Desoky GE, Wabaidur SM, AlOthman ZA, Habila MA. Evaluation of Nano-curcumin effects against Tartrazine-induced abnormalities in liver and kidney histology and other biochemical parameters. Food Sci Nutr 2022; 10:1344-1356. [PMID: 35592283 PMCID: PMC9094471 DOI: 10.1002/fsn3.2790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 01/23/2022] [Accepted: 02/15/2022] [Indexed: 12/03/2022] Open
Abstract
In the current study, 40 albino male rats were investigated to evaluate the impact of Nano-curcumin (Nano-CUR) administration against Tartrazine (TZ)-induced variations in kidney and liver histology and their related functions. The liver function biomarkers are (glutamate oxaloacetate transaminase (GOT), glutamate pyruvate transaminase (GPT), alanine aminotransferase (ALT), aspartate aminotransferase (AST), gamma-glutamyl transaminase (GGT), alkaline phosphatase (ALP), total bilirubin (T. BiLL)), whereas the kidney biomarkers are (creatinine, uric acid, urea, globulin, total protein (TP)), as well as blood parameters of (serum glucose (sGlu), alpha-fetoprotein (AFP), protein Kinase-C (PKC)) and lipid profiles that include (total lipids (TL), triglyceride (TG), total cholesterol (TC), low-density lipoprotein-cholesterol (LDL-C), high-density L-C (HDL-C), and very-low-density L-C (VLDL-C)). The collected rats were randomly separated into four different groups (G1, G2, G3, and G4) of 10 rats each, where G1 stands for control, G2 for TZ-ingestion, G3 for Nano-CUR-ingestion, and G4 for (TZ + Nano-CUR mix.) ingestion. TZ-ingestion significantly (p < .05) increases the liver function enzymes' activity, total bilirubin and kidney biomarkers (creatinine, urea, uric acid, total protein (TP), globulin (Glu)). Also, TZ-ingestion significantly increased sGlu, PKC, AFP, as well as lipid profiles, while there were significant (p < .05) decreases in HDL-C and albumin (Alb) concentrations compared to control. Histopathological changes in liver, such as dilatation of blood sinusoids and central vein with hemorrhage and necrosis, were observed due to TZ-ingestion. Similarly, TZ-ingestion influenced kidney tissues in terms of tubular dilatation with tubular degeneration, thickened basement membrane, and dilatation of the glomerular capillaries. Markedly, the administration of Nano-CUR significantly decreased liver and kidney function enzymes as well as sGlu, AFP, and PKC, whereas it significantly increased serum Alb and HDL-C levels compared to control and TZ-ingested rats. All values arranged around normal control values. Also, the liver tissue of Nano-CUR-ingested rats showed a normal arrangement of normal blood sinusoids(s), hepatic cords, and hepatocytes as compared to controls. The same results were also found in the section of rat kidney ingested with 2.00 g of Nano-CUR/(kg B.W.) showing near-normal architecture as compared to control rats. The liver tissue of rats ingested by a mixture of (7.5 mg of TZ + 2.0 g of Nano-CUR/kg B.W.) showed little necrosis. Similarly, a section of rat kidney ingested a mixture of (7.5 mg of TZ + 2.00 g of Nano-CUR/kg B.W.) which revealed mild tubular degeneration and dilatation of the glomerular capillaries. These results support the protective and therapeutic effects of Nano-CUR on the histology of liver and kidneys and their related function biomarkers. Also, Nano-CUR corrects the imbalance in serum glucose (sGlu), AFP, PKC, and lipid profiles in TZ-ingested rats compared to control.
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Affiliation(s)
- Gaber E. El‐Desoky
- Department of ChemistryCollege of ScienceKing Saud UniversityRiyadhKingdom of Saudi Arabia
| | - Saikh M. Wabaidur
- Department of ChemistryCollege of ScienceKing Saud UniversityRiyadhKingdom of Saudi Arabia
| | - Zeid A. AlOthman
- Department of ChemistryCollege of ScienceKing Saud UniversityRiyadhKingdom of Saudi Arabia
| | - Mohamed A. Habila
- Department of ChemistryCollege of ScienceKing Saud UniversityRiyadhKingdom of Saudi Arabia
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28
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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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29
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Thomas P, Rajendran TP, Franco CMM. Cytobacts: Abundant and Diverse Vertically Seed-Transmitted Cultivation-Recalcitrant Intracellular Bacteria Ubiquitous to Vascular Plants. Front Microbiol 2022; 13:806222. [PMID: 35369514 PMCID: PMC8967353 DOI: 10.3389/fmicb.2022.806222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/26/2022] [Indexed: 11/25/2022] Open
Abstract
We have recently described ‘Cytobacts’ as abundant intracellular endophytic bacteria inhabiting live plant cells based on the observations with callus and cell suspension cultures of grapevine and other plant species with the origin ascribable to field explants. In this study, we investigated the prevalence of such cytoplasmic bacterial associations in field plants across different taxa, their cultivability, and the extent of taxonomic diversity and explored the possibility of their embryo-mediated vertical transmission. Over 100 genera of field plants were surveyed for ‘Cytobacts’ through bright-field live-cell imaging as per our previous experience using fresh tissue sections from surface-sterilized shoot-tissues with parallel cultivation-based assessments. This revealed widespread cellular bacterial associations visualized as copious motile micro-particles in the cytoplasm with no or sparse colony forming units (CFU) from the tissue-homogenates indicating their general non-cultivability. Based on the ease of detection and the abundance of ‘Cytobacts’ in fresh tissue sections, the surveyed plants were empirically classified into three groups: (i) motile bacteria detected instantly in most cells; (ii) motility not so widely observed, but seen in some cells; and (iii) only occasional motile units observed, but abundant non-motile bacterial cells present. Microscopy versus 16S-rRNA V3–V4 amplicon profiling on shoot-tip tissues of four representative plants—tomato, watermelon, periwinkle, and maize—showed high bacterial abundance and taxonomic diversity (11–15 phyla) with the dominance of Proteobacteria followed by Firmicutes/Actinobacteria, and several other phyla in minor shares. The low CFU/absence of bacterial CFU from the tissue homogenates on standard bacteriological media endorsed their cultivation-recalcitrance. Intracellular bacterial colonization implied that the associated organisms are able to transmit vertically to the next generation through the seed-embryos. Microscopy and 16S-rRNA V3–V4 amplicon/metagenome profiling of mature embryos excised from fresh watermelon seeds revealed heavy embryo colonization by diverse bacteria with sparse or no CFU. Observations with grapevine fresh fruit-derived seeds and seed-embryos endorsed the vertical transmission by diverse cultivation-recalcitrant endophytic bacteria (CREB). By and large, Proteobacteria formed the major phylum in fresh seed-embryos with varying shares of diverse phyla. Thus, we document ‘Cytobacts’ comprising diverse and vertically transmissible CREBs as a ubiquitous phenomenon in vascular plants.
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Affiliation(s)
- Pious Thomas
- Thomas Biotech & Cytobacts Centre for Biosciences, Bengaluru, India.,Division of Biotechnology, ICAR-Indian Institute of Horticultural Research, Bengaluru, India
| | - Thekepat P Rajendran
- Research Information System for Developing Countries, India Habitat Centre, New Delhi, India
| | - Christopher M M Franco
- Department of Medical Biotechnology, College of Medicine & Public Health, Flinders University, Bedford Park, Adelaide, SA, Australia
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Bacteria isolated from Triticum monococcum ssp. monococcum roots can improve wheat hologenome in agriculture. Mol Biol Rep 2022; 49:5389-5395. [PMID: 35182319 DOI: 10.1007/s11033-022-07118-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND Triticum monococcum ssp. monococcum is an ancestral wheat species originated from Karacadağ Mountain of Turkey more than ten thousand years ago. Because of environmental and anthropogenic effects, food supply and demand are not balanced. Agricultural activities such as breeding, and fertilization are important to sustain the balance. Conventional breeding and fertilization applications usually neglect contribution of plant related hologenomes in agricultural yield. The disruption of plant growth promoting microorganisms results in intensive usage of chemical fertilizers. The harmony between plant and plant-associated microorganisms is important for sustainability. In this study, isolation, biochemical characterization, and impact on plant growth parameters of natural bacteria associated with Triticum monococcum ssp. monococcum hologenome were aimed. METHODS AND RESULTS The collection of root samples and isolations of the root-associated bacterial species were carried out from local wheat lands. According to interpretation of three identification methods (MALDI-TOF, 16S rDNA, 16S-23S rDNA) eight isolates are Arthrobacter spp. ESU164, Arthrobacter spp. ESU193, Pseudomonas spp. ESU131, Pseudomonas spp. ESU141, Pseudomonas poae strain ESU182, Pseudomonas thivervalensis strain ESU192, Pseudomonas spp. ESU1531, Bacillus subtilis strain ESU181. For each isolate we investigated biochemical properties especially nitrogen fixation, phosphate solubilization, and indole-3-acetic acid production abilities. The results show that all isolates are nitrogen fixers and the best phosphate solubilizer have been reported as Pseudomonas spp. ESU131 with 2.805 ± 0.439. CONCLUSIONS All isolates are indole-3-acetic acid productors. 2 isolates affected the coleoptile lengths, 7 bacterial isolates showed statistically positive effect on root number, and 5 isolates promote the root lengths and the root fresh weights.
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George P, Gupta A, Gopal M, Thomas L, Thomas GV. Indigenous rhizobacteria possessing abiotic stress tolerant traits promote vigorous growth of coconut seedlings via increased nutrient uptake and positive plant–microbe feedback. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2022. [DOI: 10.1007/s43538-022-00067-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Wang H, Elyamine AM, Liu Y, Liu W, Chen Q, Xu Y, Peng T, Hu Z. Hyunsoonleella sp. HU1-3 Increased the Biomass of Ulva fasciata. Front Microbiol 2022; 12:788709. [PMID: 35173690 PMCID: PMC8841488 DOI: 10.3389/fmicb.2021.788709] [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: 10/03/2021] [Accepted: 12/09/2021] [Indexed: 11/13/2022] Open
Abstract
Green algae are photosynthetic organisms and play an important role in coastal environment. The microbial community on the surface of green algae has an effect on the health and nutrition of the host. However, few species of epiphytic microbiota have been reported to play a role in promoting the growth of algae. In this study, 16S rDNA sequencing was used to study the changes of microbial composition on the surface of Ulva fasciata at different growth stages. Some growth promoting bacteria were identified. The possible growth-promoting behavior of the strains were verified by co-culture of pure bacteria obtained from the surface of U. fasciata with its sterile host. Among the identified species, a new bacterial species, Hyunsoonleella sp. HU1-3 (belonging to the family Flavobacteriaceae) significantly promoted the growth of U. fasciata. The results also showed that there were many genes involved in the synthesis of growth hormone and cytokinin in the genome of Hyunsoonleella sp. HU1-3. This study identified the bacterium Hyunsoonleella sp. HU1-3 for the first time, in which this bacterium has strong growth-promoting effects on U. fasciata. Our findings not only provide insights on the establishment of the surface microbiota of U. fasciata, but also indicate that Hyunsoonleella sp. HU1-3 is one of the important species to promote the growth of U. fasciata.
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Affiliation(s)
- Han Wang
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou, China
| | - Ali Mohamed Elyamine
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou, China
| | - Yuchun Liu
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou, China
| | - Wei Liu
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou, China
| | - Qixuan Chen
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou, China
| | - Yan Xu
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou, China
- Heyuan Polytechnic, Heyuan, China
| | - Tao Peng
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou, China
| | - Zhong Hu
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
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Fournier P, Pellan L, Barroso-Bergadà D, Bohan DA, Candresse T, Delmotte F, Dufour MC, Lauvergeat V, Le Marrec C, Marais A, Martins G, Masneuf-Pomarède I, Rey P, Sherman D, This P, Frioux C, Labarthe S, Vacher C. The functional microbiome of grapevine throughout plant evolutionary history and lifetime. ADV ECOL RES 2022. [DOI: 10.1016/bs.aecr.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Rhizospheric microbiome: Bio-based emerging strategies for sustainable agriculture development and future perspectives. Microbiol Res 2021; 254:126901. [PMID: 34700186 DOI: 10.1016/j.micres.2021.126901] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 10/16/2021] [Accepted: 10/21/2021] [Indexed: 12/12/2022]
Abstract
In the light of intensification of cropping practices and changing climatic conditions, nourishing a growing global population requires optimizing environmental sustainability and reducing ecosystem impacts of food production. The use of microbiological systems to ameliorate the agricultural production in a sustainable and eco-friendly way is widespread accepted as a future key-technology. However, the multitude of interaction possibilities between the numerous beneficial microbes and plants in their habitat calls for systematic analysis and management of the rhizospheric microbiome. This review exploits present and future strategies for rhizospheric microbiome management with the aim to generate a comprehensive understanding of the known tools and techniques. Significant information on the structure and dynamics of rhizospheric microbiota of isolated microbial communities is now available. These microbial communities have beneficial effects including increased plant growth, essential nutrient acquisition, pathogens tolerance, and increased abiotic as well as biotic stress tolerance such as drought, temperature, salinity and antagonistic activities against the phyto-pathogens. A better and comprehensive understanding of the various effects and microbial interactions can be gained by application of molecular approaches as extraction of DNA/RNA and other biochemical markers to analyze microbial soil diversity. Novel techniques like interactome network analysis and split-ubiquitin system framework will enable to gain more insight into communication and interactions between the proteins from microbes and plants. The aim of the analysis tasks leads to the novel approach of Rhizosphere microbiome engineering. The capability of forming the rhizospheric microbiome in a defined way will allow combining several microbes (e.g. bacteria and fungi) for a given environment (soil type and climatic zone) in order to exert beneficial influences on specific plants. This integration will require a large-scale effort among academic researchers, industry researchers and farmers to understand and manage interactions of plant-microbiomes within modern farming systems, and is clearly a multi-domain approach and can be mastered only jointly by microbiology, mathematics and information technology. These innovations will open up a new avenue for designing and implementing intensive farming microbiome management approaches to maximize resource productivity and stress tolerance of agro-ecosystems, which in return will create value to the increasing worldwide population, for both food production and consumption.
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Identification of Type II Toxin-Antitoxin Loci in Levilactobacillus brevis. Interdiscip Sci 2021; 14:80-88. [PMID: 34664198 DOI: 10.1007/s12539-021-00486-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/30/2021] [Accepted: 10/05/2021] [Indexed: 10/20/2022]
Abstract
Levilactobacillus brevis are present in various environments, such as beer, fermented foods, silage, and animal host. Like other lactic acid bacteria, L. brevis might adopt the viable but nonculturable (VBNC) state under unfavorable conditions. The toxin-antitoxin (TA) system, known to regulate cell growth in response to environmental stresses, is found to control the dynamic of the VBNC state. Here, we investigate the type II TA locus prevalence and compare the TA diversity in L. brevis genomes. Using the TAfinder software, we identified a total of 273 putative type II TA loci in 110 replicons of 21 completely sequenced genomes. Genome size does not appear to correlate with the amount of putative type II TA in L. brevis. Besides, type II TA loci are distributed differently among the chromosomes and plasmids. The most prevalent toxin domain is MazF-like in the chromosomes, and RelE/RelE-like in the plasmids; while for antitoxin, Xre-like and Phd-like domains are the most common in the chromosomes and plasmids, respectively. We also observed a unique GNAT-like/ArsR-like TA pair that presents only in the L. brevis chromosome. Detection of 273 putative type II TA loci in 21 complete genomes of Levilactobacillus brevis.
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Persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype. THE ISME JOURNAL 2021; 15:2708-2722. [PMID: 33772106 PMCID: PMC8397763 DOI: 10.1038/s41396-021-00955-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 02/12/2021] [Accepted: 03/01/2021] [Indexed: 02/01/2023]
Abstract
The full potential of managing microbial communities to support plant health is yet-unrealized, in part because it remains difficult to ascertain which members are most important for the plant. However, microbes that consistently associate with a plant species across varied field conditions and over plant development likely engage with the host or host environment. Here, we applied abundance-occupancy concepts from macroecology to quantify the core membership of bacterial/archaeal and fungal communities in the rhizosphere of the common bean (Phaseolus vulgaris). Our study investigated the microbiome membership that persisted over multiple dimensions important for plant agriculture, including major U.S. growing regions (Michigan, Nebraska, Colorado, and Washington), plant development, annual plantings, and divergent genotypes, and also included re-analysis of public data from beans grown in Colombia. We found 48 core bacterial taxa that were consistently detected in all samples, inclusive of all datasets and dimensions. This suggests reliable enrichment of these taxa to the plant environment and time-independence of their association with the plant. More generally, the breadth of ecologically important dimensions included in this work (space, time, host genotype, and management) provides an example of how to systematically identify the most stably-associated microbiome members, and can be applied to other hosts or systems.
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Cellini A, Spinelli F, Donati I, Ryu CM, Kloepper JW. Bacterial volatile compound-based tools for crop management and quality. TRENDS IN PLANT SCIENCE 2021; 26:968-983. [PMID: 34147324 DOI: 10.1016/j.tplants.2021.05.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 05/13/2021] [Accepted: 05/19/2021] [Indexed: 05/20/2023]
Abstract
Bacteria produce a huge diversity of metabolites, many of which mediate ecological relations. Among these, volatile compounds cause broad-range effects at low doses and, therefore, may be exploited for plant defence strategies and agricultural production, but such applications are still in their early development. Here, we review the latest technologies involving the use of bacterial volatile compounds for phytosanitary inspection, biological control, plant growth promotion, and crop quality. We highlight a variety of effects with a potential applicative interest, based on either live biocontrol and/or biostimulant agents, or the isolated metabolites responsible for the interaction with hosts or competitors. Future agricultural technologies may benefit from the development of new analytical tools to understand bacterial interactions with the environment.
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Affiliation(s)
- Antonio Cellini
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Francesco Spinelli
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy.
| | - Irene Donati
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Choong-Min Ryu
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Joseph W Kloepper
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
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Elhady A, Abbasi S, Safaie N, Heuer H. Responsiveness of Elite Cultivars vs. Ancestral Genotypes of Barley to Beneficial Rhizosphere Microbiome, Supporting Plant Defense Against Root-Lesion Nematodes. FRONTIERS IN PLANT SCIENCE 2021; 12:721016. [PMID: 34490018 PMCID: PMC8418270 DOI: 10.3389/fpls.2021.721016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 07/22/2021] [Indexed: 05/12/2023]
Abstract
Harnessing plant-microbe interactions to advance crop resistance to pathogens could be a keystone in sustainable agriculture. The breeding of crops to maximize yield in intensive agriculture might have led to the loss of traits that are necessary for beneficial plant-soil feedback. In this study, we tested whether the soil microbiome can induce a stronger plant defense against root-lesion nematodes in ancestral genotypes of barley than in elite cultivars. Plants were grown in a sterile substrate with or without the inoculation of rhizosphere microbiomes, and Pratylenchus neglectus was inoculated to the roots. Unexpectedly, elite cultivars profited significantly more from the microbiome than ancestral genotypes, by the reduction of nematodes in roots and the increased shoot weight relative to control plants. The elite cultivars had higher microbial densities in the rhizosphere, which were correlated with root weight. The structure of the bacterial and fungal community of elite and ancestral genotypes differed, as compared by 16S rDNA or internal transcribed spacer amplicon profiles in denaturing gradient gel electrophoresis. The elite cultivars differed in responsiveness to the microbiome. For the most responsive cultivars Beysehir and Jolgeh, the strong microbe-induced suppression of nematodes coincided with the strongest microbe-dependent increase in transcripts of salicylic acid-regulated defense genes after nematode invasion, while the jasmonate-regulated genes LOX2 and AOS were downregulated in roots with the inoculated microbiome. The microbe-triggered modulation of defense gene expression differed significantly between elite and ancestral genotypes of barley. Soil microbiomes conditioned by maize roots suppressed the nematodes in elite cultivars, while the corresponding bulk soil microbiome did not. In conclusion, cultivars Beysehir and Jolgeh harbor the genetic background for a positive plant-microbiome feedback. Exploiting these traits in breeding for responsiveness to beneficial soil microbiomes, accompanied by soil biome management for compatible plant-microbe interactions, will support low-input agriculture and sustainability.
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Affiliation(s)
- Ahmed Elhady
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institute, Federal Research Center for Cultivated Plants, Braunschweig, Germany
- Department of Plant Protection, Faculty of Agriculture, Benha University, Benha, Egypt
| | - Sakineh Abbasi
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institute, Federal Research Center for Cultivated Plants, Braunschweig, Germany
- Department of Plant Pathology, Tarbiat Modares University, Tehran, Iran
| | - Naser Safaie
- Department of Plant Pathology, Tarbiat Modares University, Tehran, Iran
| | - Holger Heuer
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institute, Federal Research Center for Cultivated Plants, Braunschweig, Germany
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Cordovez V, Rotoni C, Dini-Andreote F, Oyserman B, Carrión VJ, Raaijmakers JM. Successive plant growth amplifies genotype-specific assembly of the tomato rhizosphere microbiome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 772:144825. [PMID: 33581524 DOI: 10.1016/j.scitotenv.2020.144825] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
Plant microbiome assembly is a spatial and dynamic process driven by root exudates and influenced by soil type, plant developmental stage and genotype. Genotype-dependent microbiome assembly has been reported for different crop plant species. Despite the effect of plant genetics on microbiome assembly, the magnitude of host control over its root microbiome is relatively small or, for many plant species, still largely unknown. Here we cultivated modern and wild tomato genotypes for four successive cycles and showed that divergence in microbiome assembly between the two genotypes was significantly amplified over time. Also, we show that the composition of the rhizosphere microbiome of modern and wild plants became more dissimilar from the initial bulk soil and from each other. Co-occurrence analyses further identified amplicon sequence variants (ASVs) associated with early and late successions of the tomato rhizosphere microbiome. Among the members of the Late Successional Rhizosphere microbiome, we observed an enrichment of ASVs belonging to the genera Acidovorax, Massilia and Rhizobium in the wild tomato rhizosphere, whereas the modern tomato rhizosphere was enriched for an ASV belonging to the genus Pseudomonas. Collectively, our approach allowed us to study the dynamics of rhizosphere microbiome over successional cultivation as well as to categorize rhizobacterial taxa for their ability to form transient or long-term associations with their host plants.
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Affiliation(s)
- Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands; Institute of Biology, Leiden University, Leiden, the Netherlands.
| | - Cristina Rotoni
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands
| | - Francisco Dini-Andreote
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands; Department of Plant Science, The Pennsylvania State University, University Park, PA, USA; Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Ben Oyserman
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands; Bioinformatics Group, Wageningen University & Research, Wageningen, the Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands; Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands; Institute of Biology, Leiden University, Leiden, the Netherlands
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Clouse KM, Wagner MR. Plant Genetics as a Tool for Manipulating Crop Microbiomes: Opportunities and Challenges. Front Bioeng Biotechnol 2021; 9:567548. [PMID: 34136470 PMCID: PMC8201784 DOI: 10.3389/fbioe.2021.567548] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 05/05/2021] [Indexed: 11/22/2022] Open
Abstract
Growing human population size and the ongoing climate crisis create an urgent need for new tools for sustainable agriculture. Because microbiomes have profound effects on host health, interest in methods of manipulating agricultural microbiomes is growing rapidly. Currently, the most common method of microbiome manipulation is inoculation of beneficial organisms or engineered communities; however, these methods have been met with limited success due to the difficulty of establishment in complex farm environments. Here we propose genetic manipulation of the host plant as another avenue through which microbiomes could be manipulated. We discuss how domestication and modern breeding have shaped crop microbiomes, as well as the potential for improving plant-microbiome interactions through conventional breeding or genetic engineering. We summarize the current state of knowledge on host genetic control of plant microbiomes, as well as the key challenges that remain.
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Affiliation(s)
- Kayla M. Clouse
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States
| | - Maggie R. Wagner
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States
- Kansas Biological Survey, University of Kansas, Lawrence, KS, United States
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Heijo G, Taulé C, Mareque C, Stefanello A, Souza EM, Battistoni F. Interaction among endophytic bacteria, sweet sorghum (Sorghum bicolor) cultivars and chemical nitrogen fertilization. FEMS Microbiol Ecol 2021; 97:6007735. [PMID: 33245748 DOI: 10.1093/femsec/fiaa245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/25/2020] [Indexed: 11/14/2022] Open
Abstract
The application of new agricultural technologies to attain sustainable production systems is necessary. The use of plant growth-promoting bacteria to improve plant growth and health has been studied for decades. This work aimed to isolate diazotrophic endophytic bacteria associated with sweet sorghum plants and study the interaction of their inoculation in combination with chemical N-fertilization on different sorghum cultivars. A bacterial collection of 181 isolates was constructed and characterized in vitro and in vivo. From that, the strains Enterobacter sp. UYSB89 and Kosakonia sp. UYSB139 were nifH+, produce IAA, defined as true endophytes and able to promote growth of two sweet sorghum under greenhouse conditions. The evaluated cultivars responded differentially to bacterial inoculation, the nitrogen fertilization doses and their interaction. Thus, plant growth is a multifactorial consequence of the interrelation between crop practices and the plant genotypes. This knowledge is a valuable factor in terms of understanding plant-bacteria endophyte interactions to preserve environmental sustainability during the implementation of agronomic practices.
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Affiliation(s)
- Gabriela Heijo
- Microbial Biochemistry and Genomics Department, Clemente Estable Biological Research Institute, Avenida Italia 3318, Montevideo, 11600, Uruguay
| | - Cecilia Taulé
- Microbial Biochemistry and Genomics Department, Clemente Estable Biological Research Institute, Avenida Italia 3318, Montevideo, 11600, Uruguay
| | - Cintia Mareque
- Microbial Biochemistry and Genomics Department, Clemente Estable Biological Research Institute, Avenida Italia 3318, Montevideo, 11600, Uruguay
| | - Adriano Stefanello
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Coronel Francisco H. dos Santos Street, Curitiba, Paraná 81531-980, Brazil
| | - Emanuel M Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Coronel Francisco H. dos Santos Street, Curitiba, Paraná 81531-980, Brazil
| | - Federico Battistoni
- Microbial Biochemistry and Genomics Department, Clemente Estable Biological Research Institute, Avenida Italia 3318, Montevideo, 11600, Uruguay
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CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems. Microorganisms 2021; 9:microorganisms9040816. [PMID: 33924343 PMCID: PMC8069376 DOI: 10.3390/microorganisms9040816] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 12/31/2022] Open
Abstract
Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.
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Abdelfattah A, Freilich S, Bartuv R, Zhimo VY, Kumar A, Biasi A, Salim S, Feygenberg O, Burchard E, Dardick C, Liu J, Khan A, Ellouze W, Ali S, Spadaro D, Torres R, Teixido N, Ozkaya O, Buehlmann A, Vero S, Mondino P, Berg G, Wisniewski M, Droby S. Global analysis of the apple fruit microbiome: are all apples the same? Environ Microbiol 2021; 23:6038-6055. [PMID: 33734550 PMCID: PMC8596679 DOI: 10.1111/1462-2920.15469] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/25/2021] [Accepted: 03/16/2021] [Indexed: 01/04/2023]
Abstract
We present the first worldwide study on the apple (Malus × domestica) fruit microbiome that examines questions regarding the composition and the assembly of microbial communities on and in apple fruit. Results revealed that the composition and structure of the fungal and bacterial communities associated with apple fruit vary and are highly dependent on geographical location. The study also confirmed that the spatial variation in the fungal and bacterial composition of different fruit tissues exists at a global level. Fungal diversity varied significantly in fruit harvested in different geographical locations and suggests a potential link between location and the type and rate of postharvest diseases that develop in each country. The global core microbiome of apple fruit was represented by several beneficial microbial taxa and accounted for a large fraction of the fruit microbial community. The study provides foundational information about the apple fruit microbiome that can be utilized for the development of novel approaches for the management of fruit quality and safety, as well as for reducing losses due to the establishment and proliferation of postharvest pathogens. It also lays the groundwork for studying the complex microbial interactions that occur on apple fruit surfaces.
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Affiliation(s)
- Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria.,Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Shiri Freilich
- Department of Natural Resources, Institute of Plant Sciences, Agricultural Research Organization, Newe Yaar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Rotem Bartuv
- Department of Natural Resources, Institute of Plant Sciences, Agricultural Research Organization, Newe Yaar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel.,Department of Postharvest Science, Agricultural Research Organization, The Volcani Institute, P.O. Box 15159, Rishon LeZion, 7505101, Israel.,The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - V Yeka Zhimo
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Institute, P.O. Box 15159, Rishon LeZion, 7505101, Israel
| | - Ajay Kumar
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Institute, P.O. Box 15159, Rishon LeZion, 7505101, Israel
| | - Antonio Biasi
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Institute, P.O. Box 15159, Rishon LeZion, 7505101, Israel
| | - Shoshana Salim
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Institute, P.O. Box 15159, Rishon LeZion, 7505101, Israel
| | - Oleg Feygenberg
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Institute, P.O. Box 15159, Rishon LeZion, 7505101, Israel
| | - Erik Burchard
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS). Appalachian Fruit Research Station, Kearneysville, West Virginia, 25430, USA
| | - Christopher Dardick
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS). Appalachian Fruit Research Station, Kearneysville, West Virginia, 25430, USA
| | - Jia Liu
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Sciences, Chongqing University of Arts and Sciences, Yongchuan, Chongquing, 402160, China
| | - Awais Khan
- Cornell University, 5 Castle Creek Drive, 112 Barton Lab, Geneva, New York, 14456, USA
| | - Walid Ellouze
- Agriculture and Agri-Food Canada, Research Farm, Vineland, Ontario, Canada
| | - Shawkat Ali
- Agriculture and Agri-Food Canada, 32 Main Street, Kentville, Nova Scotia, B4N 1J5, Canada
| | - Davide Spadaro
- Department of Agricultural, Forestry and Food Sciences (DISAFA), AGROINNOVA-Centre of Competence, University of Torino, Largo Braccini 2, Grugliasco (TO), 10095, Italy
| | - Rosario Torres
- IRTA, Parc Científic i Tecnològic de Gardeny, Fruitcentre building, Lleida, Catalonia, 25003, Spain
| | - Neus Teixido
- IRTA, Parc Científic i Tecnològic de Gardeny, Fruitcentre building, Lleida, Catalonia, 25003, Spain
| | - Okan Ozkaya
- Department of Horticulture, Faculty of Agriculture 1330, Cukurova University, Adana, Turkey
| | - Andreas Buehlmann
- Agroscope, Competence Division Plants and Plant Products, Müller-Thurgaustr 29, Wädenswil, CH-8820, Switzerland
| | - Silvana Vero
- Facultad de Química-UdeLaR Cátedra de Microbiología, Montevideo, Uruguay
| | - Pedro Mondino
- Department of Plant Protection, Faculty of Agronomy, University of the Republic, Garzón 780, Montevideo, 12900, Uruguay
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria
| | - Michael Wisniewski
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, 220 Ag Quad Ln, Blacksburg, Virginia, 24061, USA
| | - Samir Droby
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Institute, P.O. Box 15159, Rishon LeZion, 7505101, Israel
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44
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Latz MAC, Kerrn MH, Sørensen H, Collinge DB, Jensen B, Brown JKM, Madsen AM, Jørgensen HJL. Succession of the fungal endophytic microbiome of wheat is dependent on tissue-specific interactions between host genotype and environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 759:143804. [PMID: 33340856 DOI: 10.1016/j.scitotenv.2020.143804] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/12/2020] [Accepted: 10/21/2020] [Indexed: 06/12/2023]
Abstract
Fungi living inside plants affect many aspects of plant health, but little is known about how plant genotype influences the fungal endophytic microbiome. However, a deeper understanding of interactions between plant genotype and biotic and abiotic environment in shaping the plant microbiome is of significance for modern agriculture, with implications for disease management, breeding and the development of biocontrol agents. For this purpose, we analysed the fungal wheat microbiome from seed to plant to seeds and studied how different potential sources of inoculum contributed to shaping of the microbiome. We conducted a large-scale pot experiment with related wheat cultivars over one growth-season in two environments (indoors and outdoors) to disentangle the effects of host genotype, abiotic environment (temperature, humidity, precipitation) and fungi present in the seed stock, air and soil on the succession of the endophytic fungal communities in roots, flag leaves and seeds at harvest. The communities were studied with ITS1 metabarcoding and environmental climate factors were monitored during the experimental period. Host genotype, tissue type and abiotic factors influenced fungal communities significantly. The effect of host genotype was mostly limited to leaves and roots, and was location-independent. While there was a clear effect of plant genotype, the relatedness between cultivars was not reflected in the microbiome. For the phyllosphere microbiome, location-dependent weather conditions factors largely explained differences in abundance, diversity, and presence of genera containing pathogens, whereas the root communities were less affected by abiotic factors. Our findings suggest that airborne fungi are the primary inoculum source for fungal communities in aerial plant parts whereas vertical transmission is likely to be insignificant. In summary, our study demonstrates that host genotype, environment and presence of fungi in the environment shape the endophytic fungal community in wheat over a growing season.
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Affiliation(s)
- Meike A C Latz
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, 1871 Frederiksberg C, Denmark.
| | - Mads Herbert Kerrn
- Data Science Lab, Department of Mathematical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Helle Sørensen
- Data Science Lab, Department of Mathematical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - David B Collinge
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, 1871 Frederiksberg C, Denmark.
| | - Birgit Jensen
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, 1871 Frederiksberg C, Denmark.
| | - James K M Brown
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Anne Mette Madsen
- The National Research Centre for the Working Environment, 2100 Copenhagen, Denmark.
| | - Hans Jørgen Lyngs Jørgensen
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, 1871 Frederiksberg C, Denmark.
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45
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Fernández-Llamosas H, Díaz E, Carmona M. Motility, Adhesion and c-di-GMP Influence the Endophytic Colonization of Rice by Azoarcus sp. CIB. Microorganisms 2021; 9:microorganisms9030554. [PMID: 33800326 PMCID: PMC7998248 DOI: 10.3390/microorganisms9030554] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/18/2021] [Accepted: 03/05/2021] [Indexed: 01/26/2023] Open
Abstract
Proficient crop production is needed to ensure the feeding of a growing global population. The association of bacteria with plants plays an important role in the health state of the plants contributing to the increase of agricultural production. Endophytic bacteria are ubiquitous in most plant species providing, in most cases, plant promotion properties. However, the knowledge on the genetic determinants involved in the colonization of plants by endophytic bacteria is still poorly understood. In this work we have used a genetic approach based on the construction of fliM, pilX and eps knockout mutants to show that the motility mediated by a functional flagellum and the pili type IV, and the adhesion modulated by exopolysaccarides are required for the efficient colonization of rice roots by the endophyte Azoarcus sp. CIB. Moreover, we have demonstrated that expression of an exogenous diguanylate cyclase or phophodiesterase, which causes either an increase or decrease of the intracellular levels of the second messenger cyclic di-GMP (c-di-GMP), respectively, leads to a reduction of the ability of Azoarcus sp. CIB to colonize rice plants. Here we present results demonstrating the unprecedented role of the universal second messenger cyclic-di-GMP in plant colonization by an endophytic bacterium, Azoarcus sp. CIB. These studies pave the way to further strategies to modulate the interaction of endophytes with their target plant hosts.
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46
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Harman GE, Doni F, Khadka RB, Uphoff N. Endophytic strains of Trichoderma increase plants' photosynthetic capability. J Appl Microbiol 2021; 130:529-546. [PMID: 31271695 DOI: 10.1111/jam.14368] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/15/2019] [Accepted: 06/20/2019] [Indexed: 12/17/2022]
Abstract
The world faces two enormous challenges that can be met, at least in part and at low cost, by making certain changes in agricultural practices. There is need to produce enough food and fibre for a growing population in the face of adverse climatic trends, and to remove greenhouse gases to avert the worst consequences of global climate change. Improving photosynthetic efficiency of crop plants can help meet both challenges. Fortuitously, when crop plants' roots are colonized by certain root endophytic fungi in the genus Trichoderma, this induces up-regulation of genes and pigments that improve the plants' photosynthesis. Plants under physiological or environmental stress suffer losses in their photosynthetic capability through damage to photosystems and other cellular processes caused by reactive oxygen species (ROS). But certain Trichoderma strains activate biochemical pathways that reduce ROS to less harmful molecules. This and other mechanisms described here make plants more resistant to biotic and abiotic stresses. The net effect of these fungi's residence in plants is to induce greater shoot and root growth, increasing crop yields, which will raise future food production. Furthermore, if photosynthesis rates are increased, more CO2 will be extracted from the atmosphere, and enhanced plant root growth means that more sequestered C will be transferred to roots and stored in the soil. Reductions in global greenhouse gas levels can be accelerated by giving incentives for climate-friendly carbon farming and carbon cap-and-trade programmes that reward practices transferring carbon from the atmosphere into the soil, also enhancing soil fertility and agricultural production.
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Affiliation(s)
| | - F Doni
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - R B Khadka
- Department of Plant Pathology, The Ohio State University, Wooster, OH, USA
- Nepal Agricultural Research Council, Kathmandu, Nepal
| | - N Uphoff
- College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
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47
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Abdelfattah A, Wisniewski M, Schena L, Tack AJM. Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root. Environ Microbiol 2021; 23:2199-2214. [PMID: 33427409 DOI: 10.1111/1462-2920.15392] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/26/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022]
Abstract
While the environment is considered the primary origin of the plant microbiome, the potential role of seeds as a source of transmitting microorganisms has not received much attention. Here we tested the hypothesis that the plant microbiome is partially inherited through vertical transmission. An experimental culturing device was constructed to grow oak seedlings in a microbe-free environment while keeping belowground and aboveground tissues separated. The microbial communities associated with the acorn's embryo and pericarp and the developing seeding's phyllosphere and root systems were analysed using amplicon sequencing of fungal ITS and bacterial 16S rDNA. Results showed that the seed microbiome is diverse and non-randomly distributed within an acorn. The microbial composition of the phyllosphere was diverse and strongly resembled the composition found in the embryo, whereas the roots and pericarp each had a less diverse and distinct microbial community. Our findings demonstrate a high level of microbial diversity and spatial partitioning of the fungal and bacterial community within both seed and seedling, indicating inheritance, niche differentiation and divergent transmission routes for the establishment of root and phyllosphere communities.
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Affiliation(s)
- Ahmed Abdelfattah
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Michael Wisniewski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Kearneysville, West Virginia, USA
| | - Leonardo Schena
- Dipartimento di Agraria, Università Mediterranea, Reggio Calabria, Italy.,Department of Biological Sciences, Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Ayco J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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48
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Zhou SYD, Li H, Giles M, Neilson R, Yang XR, Su JQ. Microbial Flow Within an Air-Phyllosphere-Soil Continuum. Front Microbiol 2021; 11:615481. [PMID: 33584580 PMCID: PMC7873851 DOI: 10.3389/fmicb.2020.615481] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/02/2020] [Indexed: 11/13/2022] Open
Abstract
The phyllosphere is populated by numerous microorganisms. Microbes from the wider environment, i.e., air and soil, are considered key contributors to phyllosphere microbial communities, but their contribution is unclear. This study seeks to address this knowledge gap by controlling the movement of microbes along the air-phyllosphere-soil continuum. Customized equipment with dual chambers was constructed that permitted airflow to enter the first chamber while the second chamber recruited filtered microbe-free air from the initial chamber. Allium schoenoprasum (chive) and Sonchus oleraceus (sow thistle) were cultivated in both chambers, and the microbial communities from air, phyllosphere, and soil samples were characterized. Shares of microbial OTUs in the equipment suggested a potential interconnection between the air, phyllosphere, and soil system. Fast expectation-maximization microbial source tracking (FEAST) suggested that soil was the major source of airborne microbial communities. In contrast, the contribution of airborne and soil microbes to phyllosphere microbial communities of either A. schoenoprasum or S. oleraceus was limited. Notably, the soilborne microbes were the only environmental sources to phyllosphere in the second chamber and could affect the composition of phyllosphere microbiota indirectly by air flow. The current study demonstrated the possible sources of phyllosphere microbes by controlling external airborne microbes in a designed microcosm system and provided a potential strategy for recruitment for phyllosphere recruitment.
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Affiliation(s)
- Shu-Yi-Dan Zhou
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Madeline Giles
- Ecological Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
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49
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Lurthy T, Pivato B, Lemanceau P, Mazurier S. Importance of the Rhizosphere Microbiota in Iron Biofortification of Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:744445. [PMID: 34925398 PMCID: PMC8679237 DOI: 10.3389/fpls.2021.744445] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/29/2021] [Indexed: 05/13/2023]
Abstract
Increasing the iron content of plant products and iron assimilability represents a major issue for human nutrition and health. This is also a major challenge because iron is not readily available for plants in most cultivated soils despite its abundance in the Earth's crust. Iron biofortification is defined as the enhancement of the iron content in edible parts of plants. This biofortification aims to reach the objectives defined by world organizations for human nutrition and health while being environment friendly. A series of options has been proposed to enhance plant iron uptake and fight against hidden hunger, but they all show limitations. The present review addresses the potential of soil microorganisms to promote plant iron nutrition. Increasing knowledge on the plant microbiota and plant-microbe interactions related to the iron dynamics has highlighted a considerable contribution of microorganisms to plant iron uptake and homeostasis. The present overview of the state of the art sheds light on plant iron uptake and homeostasis, and on the contribution of plant-microorganism (plant-microbe and plant-plant-microbe) interactions to plant nutritition. It highlights the effects of microorganisms on the plant iron status and on the co-occurring mechanisms, and shows how this knowledge may be valued through genetic and agronomic approaches. We propose a change of paradigm based on a more holistic approach gathering plant and microbial traits mediating iron uptake. Then, we present the possible applications in plant breeding, based on plant traits mediating plant-microbe interactions involved in plant iron uptake and physiology.
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50
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Acharya B, Ingram TW, Oh Y, Adhikari TB, Dean RA, Louws FJ. Opportunities and Challenges in Studies of Host-Pathogen Interactions and Management of Verticillium dahliae in Tomatoes. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1622. [PMID: 33266395 PMCID: PMC7700276 DOI: 10.3390/plants9111622] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/14/2022]
Abstract
Tomatoes (Solanum lycopersicum L.) are a valuable horticultural crop that are grown and consumed worldwide. Optimal production is hindered by several factors, among which Verticillium dahliae, the cause of Verticillium wilt, is considered a major biological constraint in temperate production regions. V. dahliae is difficult to mitigate because it is a vascular pathogen, has a broad host range and worldwide distribution, and can persist in soil for years. Understanding pathogen virulence and genetic diversity, host resistance, and plant-pathogen interactions could ultimately inform the development of integrated strategies to manage the disease. In recent years, considerable research has focused on providing new insights into these processes, as well as the development and integration of environment-friendly management approaches. Here, we discuss the current knowledge on the race and population structure of V. dahliae, including pathogenicity factors, host genes, proteins, enzymes involved in defense, and the emergent management strategies and future research directions for managing Verticillium wilt in tomatoes.
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Affiliation(s)
- Bhupendra Acharya
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA; (B.A.); (T.W.I.); (Y.Y.O.); (R.A.D.)
| | - Thomas W. Ingram
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA; (B.A.); (T.W.I.); (Y.Y.O.); (R.A.D.)
| | - YeonYee Oh
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA; (B.A.); (T.W.I.); (Y.Y.O.); (R.A.D.)
| | - Tika B. Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA; (B.A.); (T.W.I.); (Y.Y.O.); (R.A.D.)
| | - Ralph A. Dean
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA; (B.A.); (T.W.I.); (Y.Y.O.); (R.A.D.)
| | - Frank J. Louws
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA; (B.A.); (T.W.I.); (Y.Y.O.); (R.A.D.)
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
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