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Siegieda D, Panek J, Frąc M. Ecological processes of bacterial microbiome assembly in healthy and dysbiotic strawberry farms. BMC PLANT BIOLOGY 2024; 24:692. [PMID: 39030484 PMCID: PMC11264780 DOI: 10.1186/s12870-024-05415-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 07/12/2024] [Indexed: 07/21/2024]
Abstract
The bacterial microbiome plays crucial role in plants' resistance to diseases, nutrient uptake and productivity. We examined the microbiome characteristics of healthy and unhealthy strawberry farms, focusing on soil (bulk soil, rhizosphere soil) and plant (roots and shoots). The relative abundance of most abundant taxa were correlated with the chemical soil properties and shoot niche revealed the least amount of significant correlations between the two. While alpha and beta diversities did not show differences between health groups, we identified a number of core taxa (16-59) and marker bacterial taxa for each healthy (Unclassified Tepidisphaerales, Ohtaekwangia, Hydrocarboniphaga) and dysbiotic (Udaeobacter, Solibacter, Unclassified Chitinophagales, Unclassified Nitrosomonadaceae, Nitrospira, Nocardioides, Tardiphaga, Skermanella, Pseudomonas, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Curtobacterium) niche. We also revealed selective pressure of strawberry rhizosphere soil and roots plants in unhealthy plantations increased stochastic ecological processes of bacterial microbiome assembly in shoots. Our findings contribute to understanding sustainable agriculture and plant-microbiome interactions.
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Affiliation(s)
- Dominika Siegieda
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, Lublin, Lublin, 20-290, Poland
| | - Jacek Panek
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, Lublin, Lublin, 20-290, Poland
| | - Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, Lublin, Lublin, 20-290, Poland.
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Michl K, David C, Dumont B, Mårtensson LMD, Rasche F, Berg G, Cernava T. Determining the footprint of breeding in the seed microbiome of a perennial cereal. ENVIRONMENTAL MICROBIOME 2024; 19:40. [PMID: 38886863 PMCID: PMC11184768 DOI: 10.1186/s40793-024-00584-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/08/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND Seed endophytes have a significant impact on plant health and fitness. They can be inherited and passed on to the next plant generation. However, the impact of breeding on their composition in seeds is less understood. Here, we studied the indigenous seed microbiome of a recently domesticated perennial grain crop (Intermediate wheatgrass, Thinopyrum intermedium L.) that promises great potential for harnessing microorganisms to enhance crop performance by a multiphasic approach, including amplicon and strain libraries, as well as molecular and physiological assays. RESULTS Intermediate wheatgrass seeds harvested from four field sites in Europe over three consecutive years were dominated by Proteobacteria (88%), followed by Firmicutes (10%). Pantoea was the most abundant genus and Pantoea agglomerans was identified as the only core taxon present in all samples. While bacterial diversity and species richness were similar across all accessions, the relative abundance varied especially in terms of low abundant and rare taxa. Seeds from four different breeding cycles (TLI C3, C5, C704, C801) showed significant differences in bacterial community composition and abundance. We found a decrease in the relative abundance of the functional genes nirK and nifH as well as a drop in bacterial diversity and richness. This was associated with a loss of amplicon sequence variants (ASVs) in Actinobacteria, Alphaproteobacteria, and Bacilli, which could be partially compensated in offspring seeds, which have been cultivated at a new site. Interestingly, only a subset assigned to potentially beneficial bacteria, e.g. Pantoea, Kosakonia, and Pseudomonas, was transmitted to the next plant generation or shared with offspring seeds. CONCLUSION Overall, this study advances our understanding of the assembly and transmission of endophytic seed microorganisms in perennial intermediate wheatgrass and highlights the importance of considering the plant microbiome in future breeding programs.
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Affiliation(s)
- Kristina Michl
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
| | - Christophe David
- Department of Agroecosystems, Environment and Production, ISARA, 23 rue Jean Baldassini, Lyon Cedex 07, 69364, France
| | - Benjamin Dumont
- Plant Sciences Axis, Crop Science lab, ULiege - Gembloux Agro-Bio Tech, Gembloux, B- 5030, Belgium
| | | | - Frank Rasche
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, 70593, Stuttgart, Germany
- International Institute of Tropical Agriculture, P.O. Box 30772-00100, Nairobi, Kenya
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
- Leibnitz-Institute for Agricultural Engineering, 14469, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria.
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO171BJ, UK.
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Novello G, Bona E, Nasuelli M, Massa N, Sudiro C, Campana DC, Gorrasi S, Hochart ML, Altissimo A, Vuolo F, Gamalero E. The Impact of Nitrogen-Fixing Bacteria-Based Biostimulant Alone or in Combination with Commercial Inoculum on Tomato Native Rhizosphere Microbiota and Production: An Open-Field Trial. BIOLOGY 2024; 13:400. [PMID: 38927280 PMCID: PMC11200462 DOI: 10.3390/biology13060400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024]
Abstract
The agricultural sector is currently encountering significant challenges due to the effects of climate change, leading to negative consequences for crop productivity and global food security. In this context, traditional agricultural practices have been inadequate in addressing the fast-evolving challenges while maintaining environmental sustainability. A possible alternative to traditional agricultural management is represented by using beneficial micro-organisms that, once applied as bioinoculants, may enhance crop resilience and adaptability, thereby mitigating the adverse effects of environmental stressors and boosting productivity. Tomato is one of the most important crops worldwide, playing a central role in the human diet. The aim of this study was to evaluate the impact of a nitrogen-fixing bacterial-based biostimulant (Azospirillum sp., Azotobacter sp., and Rhizobium sp.) in combination or not with a commercial inoculum Micomix (Rhizoglomus irregulare, Funnelliformis mosseae, Funnelliformis caledonium, Bacillus licheniformis, and Bacillus mucilaginosus) (MYC) on the native rhizosphere communities and tomato production. Bacterial populations in the different samples were characterized using an environmental metabarcoding approach. The bioinocula effect on the native rhizosphere microbiota resulted in significant variation both in alpha and beta diversity and in a specific signature associated with the presence of biostimulants.
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Affiliation(s)
- Giorgia Novello
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, 15121 Alessandria, Italy; (G.N.); (N.M.); (D.C.C.); (E.G.)
| | - Elisa Bona
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica (DISSTE), Università del Piemonte Orientale, 13100 Vercelli, Italy;
- Center on Autoimmune and Allergic Diseases (CAAD), Università del Piemonte Orientale, 28100 Novara, Italy
| | - Martina Nasuelli
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica (DISSTE), Università del Piemonte Orientale, 13100 Vercelli, Italy;
| | - Nadia Massa
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, 15121 Alessandria, Italy; (G.N.); (N.M.); (D.C.C.); (E.G.)
| | - Cristina Sudiro
- Landlab S.r.l., 36050 Quinto Vicentino, Italy; (C.S.); (M.L.H.); (A.A.)
| | - Daniela Cristina Campana
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, 15121 Alessandria, Italy; (G.N.); (N.M.); (D.C.C.); (E.G.)
| | - Susanna Gorrasi
- Dipartimento di Scienze Ecologiche e Biologiche, Università degli Studi della Tuscia, 01100 Viterbo, Italy;
| | | | - Adriano Altissimo
- Landlab S.r.l., 36050 Quinto Vicentino, Italy; (C.S.); (M.L.H.); (A.A.)
| | | | - Elisa Gamalero
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, 15121 Alessandria, Italy; (G.N.); (N.M.); (D.C.C.); (E.G.)
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Tran DT, Mitchum MG, Zhang S, Wallace JG, Li Z. Soybean microbiome composition and the impact of host plant resistance. FRONTIERS IN PLANT SCIENCE 2024; 14:1326882. [PMID: 38288404 PMCID: PMC10822979 DOI: 10.3389/fpls.2023.1326882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/14/2023] [Indexed: 01/31/2024]
Abstract
Microbial communities play an important role in the growth and development of plants, including plant immunity and the decomposition of complex substances into absorbable nutrients. Hence, utilizing beneficial microbes becomes a promising strategy for the optimization of plant growth. The objective of this research was to explore the root bacterial profile across different soybean genotypes and the change in the microbial community under soybean cyst nematode (SCN) infection in greenhouse conditions using 16S rRNA sequencing. Soybean genotypes with soybean cyst nematode (SCN) susceptible and resistant phenotypes were grown under field and greenhouse conditions. Bulked soil, rhizosphere, and root samples were collected from each replicate. Sequencing of the bacterial 16S gene indicated that the bacterial profile of soybean root and soil samples partially overlapped but also contained different communities. The bacterial phyla Proteobacteria, Actinobacteria, and Bacteroidetes dominate the soybean root-enriched microbiota. The structure of bacteria was significantly affected by sample year (field) or time point (greenhouse). In addition, the host genotype had a small but significant effect on the diversity of the root microbiome under SCN pressure in the greenhouse test. These differences may potentially represent beneficial bacteria or secondary effects related to SCN resistance.
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Affiliation(s)
- Dung T. Tran
- Department of Crop and Soil Sciences, and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Melissa G. Mitchum
- Department of Plant Pathology, and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Shuzhen Zhang
- Department of Crop and Soil Sciences, and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Soybean Research Institute, Northeast Agricultural University, Harbin, China
| | - Jason G. Wallace
- Department of Crop and Soil Sciences, and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Zenglu Li
- Department of Crop and Soil Sciences, and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
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De-la-Vega-Camarillo E, Hernández-García JA, Villa-Tanaca L, Hernández-Rodríguez C. Unlocking the hidden potential of Mexican teosinte seeds: revealing plant growth-promoting bacterial and fungal biocontrol agents. FRONTIERS IN PLANT SCIENCE 2023; 14:1247814. [PMID: 37860235 PMCID: PMC10582567 DOI: 10.3389/fpls.2023.1247814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/15/2023] [Indexed: 10/21/2023]
Abstract
The bacterial component of plant holobiont maintains valuable interactions that contribute to plants' growth, adaptation, stress tolerance, and antagonism to some phytopathogens. Teosinte is the grass plant recognized as the progenitor of modern maize, domesticated by pre-Hispanic civilizations around 9,000 years ago. Three teosinte species are recognized: Zea diploperennis, Zea perennis, and Zea mays. In this work, the bacterial diversity of three species of Mexican teosinte seeds was explored by massive sequencing of 16S rRNA amplicons. Streptomyces, Acinetobacter, Olivibacter, Erwinia, Bacillus, Pseudomonas, Cellvibrio, Achromobacter, Devosia, Lysobacter, Sphingopyxis, Stenotrophomonas, Ochrobactrum, Delftia, Lactobacillus, among others, were the bacterial genera mainly represented. The bacterial alpha diversity in the seeds of Z. diploperennis was the highest, while the alpha diversity in Z. mays subsp. mexicana race was the lowest observed among the species and races. The Mexican teosintes analyzed had a core bacteriome of 38 bacterial genera, including several recognized plant growth promoters or fungal biocontrol agents such as Agrobacterium, Burkholderia, Erwinia, Lactobacillus, Ochrobactrum, Paenibacillus, Pseudomonas, Sphingomonas, Streptomyces, among other. Metabolic inference analysis by PICRUSt2 of bacterial genera showed several pathways related to plant growth promotion (PGP), biological control, and environmental adaptation. The implications of these findings are far-reaching, as they highlight the existence of an exceptional bacterial germplasm reservoir teeming with potential plant growth promotion bacteria (PGPB). This reserve holds the key to cultivating innovative bioinoculants and formidable fungal antagonistic strains, thereby paving the way for a more sustainable and eco-friendly approach to agriculture. Embracing these novel NGS-based techniques and understanding the profound impact of the vertical transference of microorganisms from seeds could revolutionize the future of agriculture and develop a new era of symbiotic harmony between plants and microbes.
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Affiliation(s)
| | | | | | - César Hernández-Rodríguez
- Laboratorio de Biología Molecular de Bacterias y Levaduras, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
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Ayaz M, Li CH, Ali Q, Zhao W, Chi YK, Shafiq M, Ali F, Yu XY, Yu Q, Zhao JT, Yu JW, Qi RD, Huang WK. Bacterial and Fungal Biocontrol Agents for Plant Disease Protection: Journey from Lab to Field, Current Status, Challenges, and Global Perspectives. Molecules 2023; 28:6735. [PMID: 37764510 PMCID: PMC10537577 DOI: 10.3390/molecules28186735] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/16/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023] Open
Abstract
Plants are constantly exposed to various phytopathogens such as fungi, Oomycetes, nematodes, bacteria, and viruses. These pathogens can significantly reduce the productivity of important crops worldwide, with annual crop yield losses ranging from 20% to 40% caused by various pathogenic diseases. While the use of chemical pesticides has been effective at controlling multiple diseases in major crops, excessive use of synthetic chemicals has detrimental effects on the environment and human health, which discourages pesticide application in the agriculture sector. As a result, researchers worldwide have shifted their focus towards alternative eco-friendly strategies to prevent plant diseases. Biocontrol of phytopathogens is a less toxic and safer method that reduces the severity of various crop diseases. A variety of biological control agents (BCAs) are available for use, but further research is needed to identify potential microbes and their natural products with a broad-spectrum antagonistic activity to control crop diseases. This review aims to highlight the importance of biocontrol strategies for managing crop diseases. Furthermore, the role of beneficial microbes in controlling plant diseases and the current status of their biocontrol mechanisms will be summarized. The review will also cover the challenges and the need for the future development of biocontrol methods to ensure efficient crop disease management for sustainable agriculture.
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Affiliation(s)
- Muhammad Ayaz
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230041, China; (M.A.); (W.Z.); (Y.-K.C.)
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.-Y.Y.); (Q.Y.); (J.-T.Z.); (J.-W.Y.)
| | - Cai-Hong Li
- Cotton Sciences Research Institute of Hunan, Changde 415101, China;
| | - Qurban Ali
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China;
| | - Wei Zhao
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230041, China; (M.A.); (W.Z.); (Y.-K.C.)
| | - Yuan-Kai Chi
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230041, China; (M.A.); (W.Z.); (Y.-K.C.)
| | - Muhammad Shafiq
- Biology Department and Institute of Marine Sciences, College of Science, Shantou University, Shantou 515063, China;
| | - Farman Ali
- Department of Entomology, Abdul Wali Khan University, Mardan 23200, Pakistan;
| | - Xi-Yue Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.-Y.Y.); (Q.Y.); (J.-T.Z.); (J.-W.Y.)
| | - Qing Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.-Y.Y.); (Q.Y.); (J.-T.Z.); (J.-W.Y.)
| | - Jing-Tian Zhao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.-Y.Y.); (Q.Y.); (J.-T.Z.); (J.-W.Y.)
| | - Jing-Wen Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.-Y.Y.); (Q.Y.); (J.-T.Z.); (J.-W.Y.)
| | - Ren-De Qi
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230041, China; (M.A.); (W.Z.); (Y.-K.C.)
| | - Wen-Kun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.-Y.Y.); (Q.Y.); (J.-T.Z.); (J.-W.Y.)
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Fuller E, Germaine KJ, Rathore DS. The Good, the Bad, and the Useable Microbes within the Common Alder ( Alnus glutinosa) Microbiome-Potential Bio-Agents to Combat Alder Dieback. Microorganisms 2023; 11:2187. [PMID: 37764031 PMCID: PMC10535473 DOI: 10.3390/microorganisms11092187] [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: 07/17/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Common Alder (Alnus glutinosa (L.) Gaertn.) is a tree species native to Ireland and Europe with high economic and ecological importance. The presence of Alder has many benefits including the ability to adapt to multiple climate types, as well as aiding in ecosystem restoration due to its colonization capabilities within disturbed soils. However, Alder is susceptible to infection of the root rot pathogen Phytophthora alni, amongst other pathogens associated with this tree species. P. alni has become an issue within the forestry sector as it continues to spread across Europe, infecting Alder plantations, thus affecting their growth and survival and altering ecosystem dynamics. Beneficial microbiota and biocontrol agents play a crucial role in maintaining the health and resilience of plants. Studies have shown that beneficial microbes promote plant growth as well as aid in the protection against pathogens and abiotic stress. Understanding the interactions between A. glutinosa and its microbiota, both beneficial and pathogenic, is essential for developing integrated management strategies to mitigate the impact of P. alni and maintain the health of Alder trees. This review is focused on collating the relevant literature associated with Alder, current threats to the species, what is known about its microbial composition, and Common Alder-microbe interactions that have been observed worldwide to date. It also summarizes the beneficial fungi, bacteria, and biocontrol agents, underpinning genetic mechanisms and secondary metabolites identified within the forestry sector in relation to the Alder tree species. In addition, biocontrol mechanisms and microbiome-assisted breeding as well as gaps within research that require further attention are discussed.
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Affiliation(s)
- Emma Fuller
- EnviroCore, Dargan Research Centre, Department of Applied Science, South East Technological University, Kilkenny Road, R93 V960 Carlow, Ireland; (E.F.); (K.J.G.)
- Teagasc, Forestry Development Department, Oak Park Research Centre, R93 XE12 Carlow, Ireland
| | - Kieran J. Germaine
- EnviroCore, Dargan Research Centre, Department of Applied Science, South East Technological University, Kilkenny Road, R93 V960 Carlow, Ireland; (E.F.); (K.J.G.)
| | - Dheeraj Singh Rathore
- Teagasc, Forestry Development Department, Oak Park Research Centre, R93 XE12 Carlow, Ireland
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Monteoliva MI, Ruiz OA, Li F. Editorial: Legumes and their microbiome in climate change mitigation. FRONTIERS IN PLANT SCIENCE 2023; 14:1220535. [PMID: 37377800 PMCID: PMC10291733 DOI: 10.3389/fpls.2023.1220535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023]
Affiliation(s)
- Mariela I. Monteoliva
- Instituto de Fisiología y Recursos genéticos Vegetales, Unidad de Estudios Agropecuarios (IFRGV-UDEA), Instituto Nacional de Tecnología Agropecuaria (INTA), Concejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
- Facultad de Ciencias Agropecuarias, Universidad Católica de Córdoba (UCC), Córdoba, Argentina
| | - Oscar A. Ruiz
- Universidad Nacional de San Martín (UNSAM), San Martín, Argentina
- Instituto Tecnológico de Chascomús (INTECH), CONICET, Chascomús, Argentina
| | - Fadong Li
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences (CAS), Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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