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Beattie GA, Bayliss KL, Jacobson DA, Broglie R, Burkett-Cadena M, Sessitsch A, Kankanala P, Stein J, Eversole K, Lichens-Park A. From Microbes to Microbiomes: Applications for Plant Health and Sustainable Agriculture. PHYTOPATHOLOGY 2024; 114:1742-1752. [PMID: 38776137 DOI: 10.1094/phyto-02-24-0054-kc] [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: 08/22/2024]
Abstract
Plant-microbe interaction research has had a transformative trajectory, from individual microbial isolate studies to comprehensive analyses of plant microbiomes within the broader phytobiome framework. Acknowledging the indispensable role of plant microbiomes in shaping plant health, agriculture, and ecosystem resilience, we underscore the urgent need for sustainable crop production strategies in the face of contemporary challenges. We discuss how the synergies between advancements in 'omics technologies and artificial intelligence can help advance the profound potential of plant microbiomes. Furthermore, we propose a multifaceted approach encompassing translational considerations, transdisciplinary research initiatives, public-private partnerships, regulatory policy development, and pragmatic expectations for the practical application of plant microbiome knowledge across diverse agricultural landscapes. We advocate for strategic collaboration and intentional transdisciplinary efforts to unlock the benefits offered by plant microbiomes and address pressing global issues in food security. By emphasizing a nuanced understanding of plant microbiome complexities and fostering realistic expectations, we encourage the scientific community to navigate the transformative journey from discoveries in the laboratory to field applications. As companies specializing in agricultural microbes and microbiomes undergo shifts, we highlight the necessity of understanding how to approach sustainable agriculture with site-specific management solutions. While cautioning against overpromising, we underscore the excitement of exploring the many impacts of microbiome-plant interactions. We emphasize the importance of collaborative endeavors with societal partners to accelerate our collective capacity to harness the diverse and yet-to-be-discovered beneficial activities of plant microbiomes.
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Affiliation(s)
- Gwyn A Beattie
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50014, U.S.A
| | - Kirsty L Bayliss
- Food Futures Institute, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Daniel A Jacobson
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37830, U.S.A
| | - Richard Broglie
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
| | | | - Angela Sessitsch
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
- Bioresources Unit, AIT Austrian Institute of Technology, 3430 Tulln, Austria
| | | | - Joshua Stein
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
- Eversole Associates, Arlington, MA 02476, U.S.A
| | - Kellye Eversole
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
- Eversole Associates, Arlington, MA 02476, U.S.A
| | - Ann Lichens-Park
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
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Rajapaksha RWPM, Attanayaka DPSTG, Vivehananthan K, McNevin D. Metagenomic analysis of endophytic bacteria in seed potato ( Solanum tuberosum). Open Life Sci 2024; 19:20220897. [PMID: 39071489 PMCID: PMC11282915 DOI: 10.1515/biol-2022-0897] [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: 11/09/2023] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 07/30/2024] Open
Abstract
To date, the association of potato tuber microbiota is poorly understood. In this study, the endophytic bacterial flora of seed potato tubers was identified and the diversity of healthy and unhealthy tubers was compared. Metagenomic DNA extracted from healthy and unhealthy samples of seed potato tubers was used for the analysis of microbial communities. Next generation sequencing of the ∼460 bp v3-v4 region of the 16S rRNA gene was carried out using the Illumina Miseq platform. The data were analysed using the Divisive Amplicon Denoising Algorithm 2 pipeline. Sequence analysis of the potato metagenome identified amplicon sequence variants (ASVs) assigned to 745 different taxa belonging to eight Phyla: Firmicutes (46.2%), Proteobacteria (36.9%), Bacteroidetes (1.8%), Actinobacteria (0.1%), Tenericutes (0.005%), Saccharibacteria (0.003%), Verrucomicrobiota (0.003%), and Acidobacteria (0.001%). In healthy seed potato tubers, 55-99% of ASVs belonged to Firmicutes, including Bacillus, Salinibacillus, Staphylococcus, Lysinibacillus, Paenibacillus, and Brevibacillus genera within the taxonomic order Bacillales. However, in the visually unhealthy tubers, only 0.5-3.9% of ASVs belonged to Firmicutes while 84.1-97% of ASVs belonged to Proteobacteria. This study highlights that diverse bacterial communities colonize potato tubers, which contributes to the understanding of plant-microbe interactions and underscores the significance of metagenomic approaches in agricultural research.
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Affiliation(s)
| | | | - Kalaivani Vivehananthan
- Department of Basic Sciences, Faculty of Health Sciences, The Open University of Sri Lanka, Nawala, Nugegoda, Sri Lanka
| | - Dennis McNevin
- Centre for Forensic Science, School of Mathematical & Physical Sciences, Faculty of Science, University of Technology Sydney, Sydney, Australia
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Bak GR, Lee KK, Clark IM, Mauchline TH, Kavamura VN, Lund G, Jee S, Lee JT, Kim H, Lee YH. The potato rhizosphere microbiota correlated to the yield of three different regions in Korea. Sci Rep 2024; 14:4536. [PMID: 38402369 PMCID: PMC10894198 DOI: 10.1038/s41598-024-55263-7] [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: 12/19/2023] [Accepted: 02/21/2024] [Indexed: 02/26/2024] Open
Abstract
We examined potato rhizosphere bacterial and fungal communities across three regions: Cheongju, Pyeongchang, and Gangneung. These regions have varying soil and climate conditions, resulting in different yields. We found that precipitation was the main limiting factor in our study while soil physiochemical factors affect bacterial and fungal microbiota in correlation with yield. Both bacterial and fungal microbiota showed distinct patterns according to the regions. ASVs positively correlated with yield were predominantly found in the Pyeongchang region which also produced the highest yields, while ASVs negatively correlated with yield were associated with Gangneung where the lowest yields were observed. The greatest bacterial and fungal diversity was detected in Pyeongchang consisting of Propionibacteriales, Burkholderiales, and Vicinamibacteriales. Gangneung, on the other hand primarily belong to Sordariales, Mortierellales, Cystofilobasidiales, and Tremellales. The putative yield-negative ASVs detected in Gangneung may have been influenced by drought stress. This work has highlighted key bacterial and fungal taxa as well as core taxa that may potentially be associated with high and low yields of potato in relation to metadata which includes soil chemical and physical parameters as well as weather data. Taken together we suggest that this information can be used to assess site suitability for potato production.
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Affiliation(s)
- Gye-Ryeong Bak
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
- Interdisciplinary Programs in Agricultural Genomics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kiseok Keith Lee
- Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL, 60637, USA
| | - Ian M Clark
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK
| | - Tim H Mauchline
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK
| | | | - George Lund
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK
| | - Samnyu Jee
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Jeong-Tae Lee
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
| | - Hyun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Yong-Hwan Lee
- Interdisciplinary Programs in Agricultural Genomics, Seoul National University, Seoul, 08826, Republic of Korea.
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
- Center for Plant Microbiome Research, Seoul National University, Seoul, 08826, Republic of Korea.
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea.
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Petrushin IS, Filinova NV, Gutnik DI. Potato Microbiome: Relationship with Environmental Factors and Approaches for Microbiome Modulation. Int J Mol Sci 2024; 25:750. [PMID: 38255824 PMCID: PMC10815375 DOI: 10.3390/ijms25020750] [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: 10/20/2023] [Revised: 12/12/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Every land plant exists in a close relationship with microbial communities of several niches: rhizosphere, endosphere, phyllosphere, etc. The growth and yield of potato-a critical food crop worldwide-highly depend on the diversity and structure of the bacterial and fungal communities with which the potato plant coexists. The potato plant has a specific part, tubers, and the soil near the tubers as a sub-compartment is usually called the "geocaulosphere", which is associated with the storage process and tare soil microbiome. Specific microbes can help the plant to adapt to particular environmental conditions and resist pathogens. There are a number of approaches to modulate the microbiome that provide organisms with desired features during inoculation. The mechanisms of plant-bacterial communication remain understudied, and for further engineering of microbiomes with particular features, the knowledge on the potato microbiome should be summarized. The most recent approaches to microbiome engineering include the construction of a synthetic microbial community or management of the plant microbiome using genome engineering. In this review, the various factors that determine the microbiome of potato and approaches that allow us to mitigate the negative impact of drought and pathogens are surveyed.
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Affiliation(s)
- Ivan S. Petrushin
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk 664033, Russia; (N.V.F.); (D.I.G.)
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Hanusch M, He X, Janssen S, Selke J, Trutschnig W, Junker RR. Exploring the Frequency and Distribution of Ecological Non-monotonicity in Associations among Ecosystem Constituents. Ecosystems 2023; 26:1819-1840. [PMID: 38106357 PMCID: PMC10721710 DOI: 10.1007/s10021-023-00867-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 07/06/2023] [Indexed: 12/19/2023]
Abstract
Complex links between biotic and abiotic constituents are fundamental for the functioning of ecosystems. Although non-monotonic interactions and associations are known to increase the stability, diversity, and productivity of ecosystems, they are frequently ignored by community-level standard statistical approaches. Using the copula-based dependence measure qad, capable of quantifying the directed and asymmetric dependence between variables for all forms of (functional) relationships, we determined the proportion of non-monotonic associations between different constituents of an ecosystem (plants, bacteria, fungi, and environmental parameters). Here, we show that up to 59% of all statistically significant associations are non-monotonic. Further, we show that pairwise associations between plants, bacteria, fungi, and environmental parameters are specifically characterized by their strength and degree of monotonicity, for example, microbe-microbe associations are on average stronger than and differ in degree of non-monotonicity from plant-microbe associations. Considering directed and non-monotonic associations, we extended the concept of ecosystem coupling providing more complete insights into the internal order of ecosystems. Our results emphasize the importance of ecological non-monotonicity in characterizing and understanding ecosystem patterns and processes. Supplementary Information The online version contains supplementary material available at 10.1007/s10021-023-00867-9.
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Affiliation(s)
- Maximilian Hanusch
- Department of Environment and Biodiversity, Paris-Lodron-University Salzburg, 5020 Salzburg, Austria
| | - Xie He
- Department of Environment and Biodiversity, Paris-Lodron-University Salzburg, 5020 Salzburg, Austria
| | - Stefan Janssen
- Algorithmic Bioinformatics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
| | - Julian Selke
- Algorithmic Bioinformatics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
| | - Wolfgang Trutschnig
- Department for Artificial Intelligence & Human Interfaces, Paris-Lodron-University Salzburg, 5020 Salzburg, Austria
| | - Robert R. Junker
- Department of Environment and Biodiversity, Paris-Lodron-University Salzburg, 5020 Salzburg, Austria
- Evolutionary Ecology of Plants, Department of Biology, Philipps-University Marburg, 35043 Marburg, Germany
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Effect of Abscisic Acid on Growth, Fatty Acid Profile, and Pigment Composition of the Chlorophyte Chlorella (Chromochloris) zofingiensis and Its Co-Culture Microbiome. Life (Basel) 2023; 13:life13020452. [PMID: 36836809 PMCID: PMC9962398 DOI: 10.3390/life13020452] [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: 12/21/2022] [Revised: 01/20/2023] [Accepted: 01/28/2023] [Indexed: 02/09/2023] Open
Abstract
Microalga Chlorella (Chromochloris) zofingiensis has been gaining increasing attention of investigators as a potential competitor to Haematococcus pluvialis for astaxanthin and other xanthophylls production. Phytohormones, including abscisic acid (ABA), at concentrations relevant to that in hydroponic wastewater, have proven themselves as strong inductors of microalgae biomass productivity and biosynthesis of valuable molecules. The main goal of this research was to evaluate the influence of phytohormone ABA on the physiology of C. zofingiensis in a non-aseptic batch experiment. Exogenous ABA stimulated C. zofingiensis cell division, biomass production, as well as chlorophyll, carotenoid, and lipid biosynthesis. The relationship between exogenous ABA concentration and the magnitude of the observed effects was non-linear, with the exception of cell growth and biomass production. Fatty acid accumulation and composition depended on the concentration of ABA tested. Exogenous ABA induced spectacular changes in the major components of the culture microbiome of C. zofingiensis. Thus, the abundance of the representatives of the genus Rhodococcus increased drastically with an increase in ABA concentration, whereas the abundance of the representatives of Reyranella and Bradyrhizobium genera declined. The possibilities of exogenous ABA applications for the enhancing of the biomass, carotenoid, and fatty acid productivity of the C. zofingiensis cultures are discussed.
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Shirazi K, Ketabchi S, Kargar M. Screening of endophytic bacteria from potato tubers and their antagonistic activity against soil-borne potato pathogens. JOURNAL OF BIOLOGICAL RESEARCH - BOLLETTINO DELLA SOCIETÀ ITALIANA DI BIOLOGIA SPERIMENTALE 2022. [DOI: 10.4081/jbr.2023.10625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In order to appraise the bacterial endophyte communities that help resist disease in potato tuber, the separation, the population density, biodiversity and the antagonistic activity of endophytic bacteria, from the tuber peel of potato cultivars (Fontan90, Agria, Sante’a and Jeli89), were examined in the Fars province in Iran. In this study, the bacterial endophyte Colony Forming Units (CFU) were counted based on the most suitable dilution in petri dishes and expressed per g of wet weight of tuber tissue. The presence of bacteria was found mostly in the outer layer. A wide variety of endophyte species biodiversity was in Agria cultivar. To estimate the antagonistic effect of potato associated endophytic bacteria, 115 bacterial isolates were evaluated by dual culture method against main soil-borne potato pathogens Fusarium oxysporum, Rhizoctonia solani, Verticillium dahliae, Streptomyces scabies and Ralstonia solanacearum. Endophyte strains were identified based on physiological, morphological and chemical characteristics and the 16S rRNA gene sequence analysis. The highest degree of the inhibitory activity in all layers of potato cultivars was related to Bacillus subtilis, Bacillus mojavensis and Klebsiella variicola. Antagonistic activity of endophytic bacteria against the pathogens was significantly higher (p<0.01) in the examined strains from the outermost layer of tuber peel and decreased progressively toward the center of the tuber. In this research, Klebsiella variicola was reported as endophyte bacteria in the four commercial potatocultivars mentioned above, for the first time.
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Perazzolli M, Vicelli B, Antonielli L, Longa CMO, Bozza E, Bertini L, Caruso C, Pertot I. Simulated global warming affects endophytic bacterial and fungal communities of Antarctic pearlwort leaves and some bacterial isolates support plant growth at low temperatures. Sci Rep 2022; 12:18839. [PMID: 36336707 PMCID: PMC9637742 DOI: 10.1038/s41598-022-23582-2] [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: 07/04/2022] [Accepted: 11/02/2022] [Indexed: 11/07/2022] Open
Abstract
Antarctica is one of the most stressful environments for plant life and the Antarctic pearlwort (Colobanthus quitensis) is adapted to the hostile conditions. Plant-associated microorganisms can contribute to plant survival in cold environments, but scarce information is available on the taxonomic structure and functional roles of C. quitensis-associated microbial communities. This study aimed at evaluating the possible impacts of climate warming on the taxonomic structure of C. quitensis endophytes and at investigating the contribution of culturable bacterial endophytes to plant growth at low temperatures. The culture-independent analysis revealed changes in the taxonomic structure of bacterial and fungal communities according to plant growth conditions, such as the collection site and the presence of open-top chambers (OTCs), which can simulate global warming. Plants grown inside OTCs showed lower microbial richness and higher relative abundances of biomarker bacterial genera (Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Aeromicrobium, Aureimonas, Hymenobacter, Novosphingobium, Pedobacter, Pseudomonas and Sphingomonas) and fungal genera (Alternaria, Cistella, and Vishniacozyma) compared to plants collected from open areas (OA), as a possible response to global warming simulated by OTCs. Culturable psychrotolerant bacteria of C. quitensis were able to endophytically colonize tomato seedlings and promote shoot growth at low temperatures, suggesting their potential contribution to plant tolerance to cold conditions.
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Affiliation(s)
- Michele Perazzolli
- grid.11696.390000 0004 1937 0351Centre Agriculture, Food and the Environment (C3A), University of Trento, Via E. Mach 1, 38098 San Michele all’Adige, Italy ,grid.424414.30000 0004 1755 6224Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy
| | - Bianca Vicelli
- grid.11696.390000 0004 1937 0351Centre Agriculture, Food and the Environment (C3A), University of Trento, Via E. Mach 1, 38098 San Michele all’Adige, Italy
| | - Livio Antonielli
- grid.4332.60000 0000 9799 7097Center for Health and Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430 Tulln an der Donau, Austria
| | - Claudia M. O. Longa
- grid.424414.30000 0004 1755 6224Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy
| | - Elisa Bozza
- grid.424414.30000 0004 1755 6224Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy
| | - Laura Bertini
- grid.12597.380000 0001 2298 9743Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università s.n.c., 01100 Viterbo, Italy
| | - Carla Caruso
- grid.12597.380000 0001 2298 9743Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università s.n.c., 01100 Viterbo, Italy
| | - Ilaria Pertot
- grid.11696.390000 0004 1937 0351Centre Agriculture, Food and the Environment (C3A), University of Trento, Via E. Mach 1, 38098 San Michele all’Adige, Italy ,grid.424414.30000 0004 1755 6224Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098 San Michele all’Adige, Italy
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Du G, Sun Z, Bao S, Zhong Q, Yang S. Diversity of bacterial community in Jerusalem artichoke (Helianthus tuberosus L.) during storage is associated with the genotype and carbohydrates. Front Microbiol 2022; 13:986659. [PMID: 36187957 PMCID: PMC9520535 DOI: 10.3389/fmicb.2022.986659] [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: 07/05/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
Jerusalem artichoke (JA) is a fructan-accumulating crop that has gained popularity in recent years. The objective of the present study was to determine the dynamics of the JA-microbiome during storage. The microbial population on the surface of the JA tuber was determined by next-generation sequencing of 16S rRNA amplicons. Subsequently, the changes in carbohydrate and degree of polymerization of fructan in tubers during storage were measured. Among different genotypes of JA varieties, intergeneric differences were observed in the diversity and abundance of bacterial communities distributed on the surface of tubers. Additionally, bacterial diversity was significantly higher in storage-tolerant varieties relative to the storage-intolerant varieties. Redundancy analysis (RDA) and the correlation matrix indicated a relationship between changes in the carbohydrates and microbial community succession during tuber storage. The tuber decay rate correlated positively with the degree of polymerization of fructan. Moreover, Dysgonomonas and Acinetobacter in perishable varieties correlated significantly with the decay rate. Therefore, the bacteria associated with the decay rate may be involved in the degradation of the degree of polymerization of fructan. Furthermore, Serratia showed a significant positive correlation with inulin during storage but a negative correlation with the decay rate, suggesting its antagonistic role against pathogenic bacteria on the surface of JA tubers. However, the above correlation was not observed in the storage-tolerant varieties. Functional annotation analysis revealed that storage-tolerant JA varieties maintain tuber quality through enrichment of biocontrol bacteria, including Flavobacterium, Sphingobacterium, and Staphylococcus to resist pathogens. These results suggested that crop genotype and the structural composition of carbohydrates may result in differential selective enrichment effects of microbial communities on the surface of JA varieties. In this study, the relationship between microbial community succession and changes in tuber carbohydrates during JA storage was revealed for the first time through the combination of high-throughput sequencing, high-performance liquid chromatography (HPLC), and high-performance ion-exchange chromatography (HPIC). Overall, the findings of this study are expected to provide new insights into the dynamics of microbial-crop interactions during storage.
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Affiliation(s)
- Guolian Du
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Agriculture and Forestry Sciences Institute of Qinghai University, Qinghai University, Xining, China
| | - Zhu Sun
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Agriculture and Forestry Sciences Institute of Qinghai University, Qinghai University, Xining, China
| | - Shanhua Bao
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Agriculture and Forestry Sciences Institute of Qinghai University, Qinghai University, Xining, China
| | - Qiwen Zhong
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Agriculture and Forestry Sciences Institute of Qinghai University, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Qinghai University, Xining, China
- *Correspondence: Qiwen Zhong,
| | - Shipeng Yang
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Agriculture and Forestry Sciences Institute of Qinghai University, Qinghai University, Xining, China
- Shipeng Yang,
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Huang K, Sun X, Zou Y, Li H, Xu P, Zhang W, Zhang Y, Li H, Sun H, Wang W, Pang M, Luo J. Comparison of the Endophytic Bacterial Microbiota of Asymptomatic and Symptomatic Ginger Rhizomes During the Activation of Adventitious Bud Development. PLANT DISEASE 2022; 106:2470-2479. [PMID: 35286131 DOI: 10.1094/pdis-09-21-2069-re] [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: 06/14/2023]
Abstract
Bacterial infections are the cause of rhizome rot in ginger (Zingiber officinale). Key members of the endophytic microbial community in ginger rhizomes have not been identified, and their impact on the decay of rhizomes during the activation of adventitious bud development has not been investigated. High-throughput, 16S rRNA amplicon sequencing and inoculation experiments were used to analyze the microbial diversity, community structure and composition, and pathogenicity of isolated bacteria. Our results indicated that the composition of the endophytic microbiota underwent a shift during the progression of rhizome rot disease. Enterobacteriaceae, Lachnospiraceae, and the bacterial genera Clostridium, Bacteroides, Acrobacter, Dysgonomonas, Anaerosinus, Pectobacterium, and Lactococcus were relatively abundant in the bacterial community of rhizomes exhibiting bacterial decay symptoms but were also present in asymptomatic rhizomes. The presence of Enterobacteriaceae and Pseudomonadaceae were positively correlated (ρ = 0.83) at the beginning of the sampling period in the symptomatic group, while a positive correlation (ρ = 0.89) was only observed after 20 days in the asymptomatic group. These data indicate that the co-occurrence of Enterobacteriaceae and Pseudomonadaceae may be associated with the development of ginger rot. Bacterial taxa isolated from ginger rhizomes, such as Enterobacter cloacae, E. hormaechei, and Pseudomonas putida, induced obvious rot symptoms when they were inoculated on ginger rhizomes. Notably, antibiotic-producing bacterial taxa in the Streptococcaceae and Flavobacteriaceae were also relatively abundant in rhizomes with rot and appeared to be linked to the onset of rhizome rot disease. Our results provide important information on the establishment and management of disease in ginger rhizomes.
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Affiliation(s)
- Ke Huang
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts & Sciences, Yongchuan, 402160, China
- Institute of Microbial Ecology, Chongqing University of Arts & Sciences, Yongchuan, 402160, China
| | - Xiangcheng Sun
- West China Biopharm Research Institute, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yong Zou
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts & Sciences, Yongchuan, 402160, China
| | - Huihe Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts & Sciences, Yongchuan, 402160, China
| | - Panpan Xu
- College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Wenlin Zhang
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts & Sciences, Yongchuan, 402160, China
| | - Yin Zhang
- Agricultural and Rural Committee of Chongqing Rongchang District, Rongchang, 402460, China
| | - Honglei Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts & Sciences, Yongchuan, 402160, China
| | - Hanchang Sun
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts & Sciences, Yongchuan, 402160, China
| | - Wei Wang
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts & Sciences, Yongchuan, 402160, China
- Institute of Microbial Ecology, Chongqing University of Arts & Sciences, Yongchuan, 402160, China
| | - Min Pang
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts & Sciences, Yongchuan, 402160, China
| | - Jie Luo
- Department of Pharmaceutical, Chongqing University of Arts and Sciences, Chongqing University of Arts & Sciences, Yongchuan, 402160, China
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Extension of Solanaceae Food Crops Shelf Life by the Use of Elicitors and Sustainable Practices During Postharvest Phase. FOOD BIOPROCESS TECH 2021. [DOI: 10.1007/s11947-021-02713-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Glick BR, Gamalero E. Recent Developments in the Study of Plant Microbiomes. Microorganisms 2021; 9:microorganisms9071533. [PMID: 34361969 PMCID: PMC8306116 DOI: 10.3390/microorganisms9071533] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/11/2021] [Accepted: 07/16/2021] [Indexed: 02/06/2023] Open
Abstract
To date, an understanding of how plant growth-promoting bacteria facilitate plant growth has been primarily based on studies of individual bacteria interacting with plants under different conditions. More recently, it has become clear that specific soil microorganisms interact with one another in consortia with the collective being responsible for the positive effects on plant growth. Different plants attract different cross-sections of the bacteria and fungi in the soil, initially based on the composition of the unique root exudates from each plant. Thus, plants mostly attract those microorganisms that are beneficial to plants and exclude those that are potentially pathogenic. Beneficial bacterial consortia not only help to promote plant growth, these consortia also protect plants from a wide range of direct and indirect environmental stresses. Moreover, it is currently possible to engineer plant seeds to contain desired bacterial strains and thereby benefit the next generation of plants. In this way, it may no longer be necessary to deliver beneficial microbiota to each individual growing plant. As we develop a better understanding of beneficial bacterial microbiomes, it may become possible to develop synthetic microbiomes where compatible bacteria work together to facilitate plant growth under a wide range of natural conditions.
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Affiliation(s)
- Bernard R. Glick
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
| | - Elisa Gamalero
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale “A. Avogadro”, Viale Teresa Michel, 11, 15121 Alessandria, Italy
- Correspondence:
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