1
|
Liu Y, Zhao K, Stirling E, Wang X, Gao Z, Ma B, Xu C, Chen S, Chu G, Zhang X, Wang D. Heterosis of endophytic microbiomes in hybrid rice varieties improves seed germination. mSystems 2024; 9:e0000424. [PMID: 38591897 PMCID: PMC11097635 DOI: 10.1128/msystems.00004-24] [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: 01/17/2024] [Accepted: 02/27/2024] [Indexed: 04/10/2024] Open
Abstract
Seed endophytic microbiomes are shaped by host and environmental factors and play a crucial role in their host growth and health. Studies have demonstrated that host genotype, including hybridization, affects seed microbiomes. Heterosis features are also observed in root-associated microbiomes. It remains unclear, however, whether heterosis exists in seed endophytic microbiomes and whether hybrid microbiota provide noticeable advantages to host plant growth, especially to seed germination. Here, we investigated the structure of seed endophytic bacterial and fungal communities from three hybrid rice varieties and their respective parents using amplicon sequencing targeting 16S rRNA and ITS2 genes. Heterosis was found in diversity and composition of seed endophytic microbiomes in hybrids, which hosted more diverse communities and significantly higher abundances of plant growth-promoting taxa, such as Pseudomonas and Rhizobium genera compared with their parental lines. Co-occurrence network analysis revealed that there are potentially tighter microbial interactions in the hybrid seeds compared with their parent seeds. Finally, inoculation of seed-cultivable endophytes, isolated from hybrids, resulted in a greater promotion of seed germination compared with those isolated from parent lines. These findings suggest that heterosis exists not only in plant traits but also in seed endophytic microbiota, the latter in turn promotes seed germination, which offers valuable guidance for microbiome-assisted rice breeding.IMPORTANCEGenetic and physiological changes associated with plant hybridization have been studied for many crop species. Still, little is known about the impact of hybridization on the seed microbiota. In this study, we indicate that hybridization has a significant impact on the endophytic bacterial and fungal communities in rice seeds. The seed endophytic microbiomes of hybrids displayed distinct characteristics from those of their parental lines and exhibited potential heterosis features. Furthermore, the inoculation of seed-cultivable endophytes isolated from hybrids exhibited a greater promotion effect on seed germination compared with those isolated from the parents. Our findings make a valuable contribution to the emerging field of microbiome-assisted plant breeding, highlighting the potential for a targeted approach that aims to achieve not only desired plant traits but also plant-beneficial microbial communities on the seeds.
Collapse
Affiliation(s)
- Yuanhui Liu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Kankan Zhao
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Erinne Stirling
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Adelaide, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Xiaolin Wang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Bin Ma
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chunmei Xu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Song Chen
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Guang Chu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Xiufu Zhang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Danying Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, Zhejiang, China
| |
Collapse
|
2
|
Cao M, Huang S, Li J, Zhang X, Zhu Y, Sun J, Zhu L, Deng Y, Xu J, Zhang Z, Li Q, Ai J, Xie T, Li H, Yin H, Kong W, Gu Y. Disease-induced changes in bacterial and fungal communities from plant below- and aboveground compartments. Appl Microbiol Biotechnol 2024; 108:315. [PMID: 38689185 PMCID: PMC11061026 DOI: 10.1007/s00253-024-13150-1] [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: 04/24/2023] [Revised: 01/31/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
The plant microbes are an integral part of the host and play fundamental roles in plant growth and health. There is evidence indicating that plants have the ability to attract beneficial microorganisms through their roots in order to defend against pathogens. However, the mechanisms of plant microbial community assembly from below- to aboveground compartments under pathogen infection remain unclear. In this study, we investigated the bacterial and fungal communities in bulk soil, rhizosphere soil, root, stem, and leaf of both healthy and infected (Potato virus Y disease, PVY) plants. The results indicated that bacterial and fungal communities showed different recruitment strategies in plant organs. The number and abundance of shared bacterial ASVs between bulk and rhizosphere soils decreased with ascending migration from below- to aboveground compartments, while the number and abundance of fungal ASVs showed no obvious changes. Field type, plant compartments, and PVY infection all affected the diversity and structures of microbial community, with stronger effects observed in the bacterial community than the fungal community. Furthermore, PVY infection, rhizosphere soil pH, and water content (WC) contributed more to the assembly of the bacterial community than the fungal community. The analysis of microbial networks revealed that the bacterial communities were more sensitive to PVY infection than the fungal communities, as evidenced by the lower network stability of the bacterial community, which was characterized by a higher proportion of positive edges. PVY infection further increased the bacterial network stability and decreased the fungal network stability. These findings advance our understanding of how microbes respond to pathogen infections and provide a rationale and theoretical basis for biocontrol technology in promoting sustainable agriculture. KEY POINTS: • Different recruitment strategies between plant bacterial and fungal communities. • Bacterial community was more sensitive to PVY infection than fungal community. • pH and WC drove the microbial community assembly under PVY infection.
Collapse
Affiliation(s)
- Mingfeng Cao
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Songqing Huang
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Jingjing Li
- Technology Center of China Tobacco Fujian Company, Xiamen, China
| | - Xiaoming Zhang
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Yi Zhu
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Jingzhao Sun
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Li Zhu
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Yong Deng
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Jianqiang Xu
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Zhihua Zhang
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Qiang Li
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Jixiang Ai
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Tian Xie
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Hengli Li
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Wuyuan Kong
- Changde Tobacco Company of Hunan Province, Changde, China.
| | - Yabing Gu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.
| |
Collapse
|
3
|
Wu CD, Fan YB, Chen X, Cao JW, Ye JY, Feng ML, Liu XX, Sun WJ, Liu RN, Wang AY. Analysis of endophytic bacterial diversity in seeds of different genotypes of cotton and the suppression of Verticillium wilt pathogen infection by a synthetic microbial community. BMC PLANT BIOLOGY 2024; 24:263. [PMID: 38594616 PMCID: PMC11005247 DOI: 10.1186/s12870-024-04910-2] [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: 01/16/2024] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND In agricultural production, fungal diseases significantly impact the yield and quality of cotton (Gossypium spp.) with Verticillium wilt posing a particularly severe threat. RESULTS This study is focused on investigating the effectiveness of endophytic microbial communities present in the seeds of disease-resistant cotton genotypes in the control of cotton Verticillium wilt. The technique of 16S ribosomal RNA (16S rRNA) amplicon sequencing identified a significant enrichment of the Bacillus genus in the resistant genotype Xinluzao 78, which differed from the endophytic bacterial community structure in the susceptible genotype Xinluzao 63. Specific enriched strains were isolated and screened from the seeds of Xinluzao 78 to further explore the biological functions of seed endophytes. A synthetic microbial community (SynCom) was constructed using the broken-rod model, and seeds of the susceptible genotype Xinluzao 63 in this community that had been soaked with the SynCom were found to significantly control the occurrence of Verticillium wilt and regulate the growth of cotton plants. Antibiotic screening techniques were used to preliminarily identify the colonization of strains in the community. These techniques revealed that the strains can colonize plant tissues and occupy ecological niches in cotton tissues through a priority effect, which prevents infection by pathogens. CONCLUSION This study highlights the key role of seed endophytes in driving plant disease defense and provides a theoretical basis for the future application of SynComs in agriculture.
Collapse
Affiliation(s)
- Chong-Die Wu
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Yong-Bin Fan
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Xue Chen
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Jiang-Wei Cao
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Jing-Yi Ye
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Meng-Lei Feng
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Xing-Xing Liu
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Wen-Jing Sun
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Rui-Na Liu
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Ai-Ying Wang
- College of Life Sciences, Shihezi University, Shihezi, China.
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China.
| |
Collapse
|
4
|
Davies J, Hawkins S, Winters A, Farrar K. Bacterial endophytic community composition varies by hemp cultivar in commercially sourced seed. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13259. [PMID: 38649235 PMCID: PMC11035101 DOI: 10.1111/1758-2229.13259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/12/2024] [Indexed: 04/25/2024]
Abstract
The seed-endophytic bacterial community is a potentially beneficial and heritable fraction of the plant microbiome. Its utilization as a sustainable crop improvement strategy could be especially valuable for species such as hemp, where production is being scaled up and new challenges will be faced in managing crop productivity and health. However, little is known about the makeup and variation of the hemp seed microbiome. This study profiled the endophytic bacterial communities harboured by 16 hemp cultivars sourced from commercial suppliers in Europe. A 16S rDNA amplicon sequencing approach identified 917 amplicon sequence variants across samples. Taxonomic classification of sequences revealed 4 phyla and 87 genera to be represented in the dataset. Several genera were widespread while some were specific to one or a few cultivars. Flavobacterium, Pseudomonas, and Pantoea were notable in their high overall abundance and prevalence, but community composition was variable and no one taxon was universally abundant, suggesting a high degree of flexibility in community assembly. Taxonomic composition and alpha diversity differed among cultivars, though further work is required to understand the relative influence of hemp genetic factors on community structure. The taxonomic profiles presented here can be used to inform further work investigating the functional characteristics and potential plant-growth-promoting traits of seed-borne bacteria in hemp.
Collapse
Affiliation(s)
- Jack Davies
- Institute of Biological, Environmental & Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| | - Sarah Hawkins
- Institute of Biological, Environmental & Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| | - Ana Winters
- Institute of Biological, Environmental & Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| | - Kerrie Farrar
- Institute of Biological, Environmental & Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| |
Collapse
|
5
|
Yao Y, Liu C, Zhang Y, Lin Y, Chen T, Xie J, Chang H, Fu Y, Cheng J, Li B, Yu X, Lyu X, Feng Y, Bian X, Jiang D. The Dynamic Changes of Brassica napus Seed Microbiota across the Entire Seed Life in the Field. PLANTS (BASEL, SWITZERLAND) 2024; 13:912. [PMID: 38592934 PMCID: PMC10975644 DOI: 10.3390/plants13060912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
The seed microbiota is an important component given by nature to plants, protecting seeds from damage by other organisms and abiotic stress. However, little is known about the dynamic changes and potential functions of the seed microbiota during seed development. In this study, we investigated the composition and potential functions of the seed microbiota of rapeseed (Brassica napus). A total of 2496 amplicon sequence variants (ASVs) belonging to 504 genera in 25 phyla were identified, and the seed microbiota of all sampling stages were divided into three groups. The microbiota of flower buds, young pods, and seeds at 20 days after flowering (daf) formed the first group; that of seeds at 30 daf, 40 daf and 50 daf formed the second group; that of mature seeds and parental seeds were clustered into the third group. The functions of seed microbiota were identified by using PICRUSt2, and it was found that the substance metabolism of seed microbiota was correlated with those of the seeds. Finally, sixty-one core ASVs, including several potential human pathogens, were identified, and a member of the seed core microbiota, Sphingomonas endophytica, was isolated from seeds and found to promote seedling growth and enhance resistance against Sclerotinia sclerotiorum, a major pathogen in rapeseed. Our findings provide a novel perspective for understanding the composition and functions of microbiota during seed development and may enhance the efficiency of mining beneficial seed microbes.
Collapse
Affiliation(s)
- Yao Yao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Changxing Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yu Zhang
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Haibin Chang
- Huanggang Academy of Agricultural Science, Huanggang 438000, China;
| | - Yanping Fu
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiao Yu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xueliang Lyu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yanbo Feng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xuefeng Bian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| |
Collapse
|
6
|
de Souza YPA, Schloter M, Weisser W, Huang Y, Schulz S. The seeds of Plantago lanceolata comprise a stable core microbiome along a plant richness gradient. ENVIRONMENTAL MICROBIOME 2024; 19:11. [PMID: 38308354 PMCID: PMC10835927 DOI: 10.1186/s40793-024-00552-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/19/2024] [Indexed: 02/04/2024]
Abstract
BACKGROUND Seed endophytic bacteria are beneficial to plants. They improve seedling growth by enhancing plant nutrient uptake, modulating stress-related phytohormone production, and targeting pests and pathogens with antibiotics. Seed endophyte composition can be influenced by pollination, plant cultivar, and soil physicochemical conditions. However, the effects of plant community richness on seed endophytes are unknown. To investigate the effects of increasing plant species richness on the diversity and composition of the seed microbiome, we made use of a well-established long-term biodiversity experiment in Germany (The Jena Experiment). We sampled seeds from different Plantago lanceolata blossoms in a plant diversity gradient ranging from monoculture to 16 species mixtures. The seeds were surface sterilized to remove seed surface-associated bacteria and subjected to a metabarcoding approach to assess bacterial community structure. RESULTS Our data indicate a very stable core microbiome, which accounted for more than 90% of the reads and was present in all seeds independent of the plant richness level the seeds originated from. It consisted mainly of reads linked to Pseudomonas rhizosphaerae, Sphingomonas faeni and Pirellulla spp. 9% of the obtained reads were not part of the core microbiome and were only present in plots of specific diversity levels. The number of unique ASVs was positively correlated with plant richness. Interestingly, most reads described as non-core members belonged to the same genera described as the core microbiome, indicating the presence of different strains or species with possibly different functional properties important for seed performance. CONCLUSION Our data indicate that Plantago lanceolata maintains a large seeds core microbiome across the plant richness gradient. However, the number of unique ASVs increases alongside the plant community richness, indicating that ecosystem biodiversity also mitigates diversity loss in seed endophytes.
Collapse
Affiliation(s)
- Yuri Pinheiro Alves de Souza
- TUM School of Life Science, Chair of Environmental Microbiology, Technische Universität München, Neuherberg, Germany
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael Schloter
- TUM School of Life Science, Chair of Environmental Microbiology, Technische Universität München, Neuherberg, Germany.
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany.
| | - Wolfgang Weisser
- TUM School of Life Science, Chair of Terrestrial Ecology, Technische Universität München, Freising, Germany
| | - Yuanyuan Huang
- German Centre of Integrative Bioaffiliationersity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Experimental Interaction Ecology, Leipzig University, Leipzig, Germany
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| |
Collapse
|
7
|
Wu PH, Chang HX. Colonization compatibility with Bacillus altitudinis confers soybean seed rot resistance. THE ISME JOURNAL 2024; 18:wrae142. [PMID: 39073909 DOI: 10.1093/ismejo/wrae142] [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: 05/10/2024] [Revised: 07/15/2024] [Accepted: 07/25/2024] [Indexed: 07/31/2024]
Abstract
The plant microbiome and plant-associated bacteria are known to support plant health, but there are limited studies on seed and seedling microbiome to reveal how seed-associated bacteria may confer disease resistance. In this study, the application of antibiotics on soybean seedlings indicated that seed-associated bacteria were involved in the seed rot resistance against a soil-borne pathogen Calonectria ilicicola, but this resistance cannot be carried to withstand root rot. Using PacBio 16S rRNA gene full-length sequencing and microbiome analyses, 14 amplicon sequence variants (ASVs) including 2 ASVs matching to Bacillus altitudinis were found to be more abundant in the four most resistant varieties versus the four most susceptible varieties. Culture-dependent isolation obtained two B. altitudinis isolates that both exhibit antagonistic capability against six fungal pathogens. Application of B. altitudinis on the most resistant and susceptible soybean varieties revealed different colonization compatibility, and the seed rot resistance was restored in the five varieties showing higher bacterial colonization. Moreover, quantitative PCR confirmed the persistence of B. altitudinis on apical shoots till 21 days post-inoculation (dpi), but 9 dpi on roots of the resistant variety TN5. As for the susceptible variety HC, the persistence of B. altitudinis was only detected before 6 dpi on both shoots and roots. The short-term colonization of B. altitudinis on roots may explain the absence of root rot resistance. Collectively, this study advances the insight of B. altitudinis conferring soybean seed rot resistance and highlights the importance of considering bacterial compatibility with plant varieties and colonization persistence on plant tissues.
Collapse
Affiliation(s)
- Ping-Hu Wu
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei City 10617, Taiwan
| | - Hao-Xun Chang
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei City 10617, Taiwan
| |
Collapse
|
8
|
Li XY, Wu WF, Wu CY, Hu Y, Xiang Q, Li G, Lin XY, Zhu YG. Seeds Act as Vectors for Antibiotic Resistance Gene Dissemination in a Soil-Plant Continuum. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21358-21369. [PMID: 38078407 DOI: 10.1021/acs.est.3c05678] [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: 12/20/2023]
Abstract
Though the evidence for antibiotic resistance spread via plant microbiome is mounting, studies regarding antibiotic resistome in the plant seed, a reproductive organ and important food resource, are still in their infancy. This study investigated the effects of long-term organic fertilization on seed bacterial endophytes, resistome, and their intergenerational transfer in the microcosm. A total of 99 antibiotic resistance genes (ARGs) and 26 mobile genetic elements (MGEs) were detected by high-throughput quantitative PCR. The amount of organic fertilizer applied was positively correlated to the number and relative abundance of seed-associated ARGs and MGEs. Moreover, the transmission of ARGs from the rhizosphere to the seed was mainly mediated by the shared bacteria and MGEs. Notably, the rhizosphere of progeny seedlings derived from seeds harboring abundant ARGs was found to have a higher relative abundance of ARGs. Using structural equation models, we further revealed that seed resistome and MGEs were key factors affecting the ARGs in the progeny rhizosphere, implying the seed was a potential resistome reservoir for rhizosphere soil. This study highlights the overlooked role of seed endophytes in the dissemination of resistome in the soil-plant continuum, and more attention should be paid to plant seeds as vectors of ARGs within the "One-Health" framework.
Collapse
Affiliation(s)
- Xin-Yuan Li
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Wei-Feng Wu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Chun-Yan Wu
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China
| | - Yan Hu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Qian Xiang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Xian-Yong Lin
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yong-Guan Zhu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| |
Collapse
|
9
|
Singh P, Vaishnav A, Liu H, Xiong C, Singh HB, Singh BK. Seed biopriming for sustainable agriculture and ecosystem restoration. Microb Biotechnol 2023; 16:2212-2222. [PMID: 37490280 PMCID: PMC10686123 DOI: 10.1111/1751-7915.14322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023] Open
Abstract
The utilization of microbial inoculants in the realm of sustainable agricultural and ecosystem restoration has witnessed a surge in recent decades. This rise is largely attributed to advancements in our understanding of plant-microbe interactions, the urgency to reduce the dependence on agrochemicals and the growing societal demand for sustainable strategies in ecosystem management. However, despite the rapid growth of bio-inoculants sector, certain limitations persist concerning their efficacy and performance under the field condition. Here, we propose that seed biopriming, an effective microbial inoculant technique integrating both biological agents (the priming of beneficial microbes on seeds) and physiological aspects (hydration of seeds for improved metabolically activity), has a significant potential to mitigate these limitations. This method increases the protection of seeds against soil-borne pathogens and soil pollutants, such as salts and heavy metals, while promoting germination rate and uniformity, leading to overall improved primary productivity and soil health. Furthermore, we argue that a microbial coating on seeds can facilitate transgenerational associations of beneficial microbes, refine plant and soil microbiomes, and maintain soil legacies of beneficial microflora. This review article aims to improve our understanding of the seed biopriming approach as a potent and valuable tool in achieving sustainable agriculture and successful ecosystem restoration.
Collapse
Affiliation(s)
- Prachi Singh
- Rabindranath Tagore Agriculture College, DeogharBirsa Agriculture UniversityRanchiJharkhandIndia
| | - Anukool Vaishnav
- Department of BiotechnologyGLA UniversityMathuraUttar PradeshIndia
| | - Hongwei Liu
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
| | - Chao Xiong
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
| | | | - Brajesh K. Singh
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
- Global Centre for Land‐Based InnovationWestern Sydney UniversityPenrithNew South WalesAustralia
| |
Collapse
|
10
|
Acuña JJ, Hu J, Inostroza NG, Valenzuela T, Perez P, Epstein S, Sessitsch A, Zhang Q, Jorquera MA. Endophytic bacterial communities in ungerminated and germinated seeds of commercial vegetables. Sci Rep 2023; 13:19829. [PMID: 37963999 PMCID: PMC10645892 DOI: 10.1038/s41598-023-47099-4] [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: 07/26/2023] [Accepted: 11/09/2023] [Indexed: 11/16/2023] Open
Abstract
Chile is a prominent seed exporter globally, but the seed microbiome of vegetables (46% of seeds) and its role in the early stages of plant growth have remained largely unexplored. Here, we employed DNA metabarcoding analysis to investigate the composition and putative functions of endophytic bacterial communities in ungerminated and germinated seeds of the commercial vegetables Apiaceae (parsley and carrot), Asteraceae (lettuce), Brassicaceae (cabbage and broccoli), and Solanaceae (tomato). Bacterial quantification showed 104 to 108 copies of the 16S rRNA gene per gram of ungerminated and germinated seeds. Alpha diversity analysis (e.g., Chao1, Shannon, and Simpson indices) did not indicate significant differences (Kruskal-Wallis test) between ungerminated and germinated seeds, except for Solanaceae. However, beta diversity (PCoA) analysis showed distinctions (Adonis test) between ungerminated and germinated seeds, except Apiaceae. Pseudomonadota and Bacillota were identified as the dominant and specialist taxa in both ungerminated and germinated seed samples. Chemoheterotrophy and fermentation were predicted as the main microbial functional groups in the endophytic bacterial community. Notably, a considerable number of the 143 isolated endophytic strains displayed plant growth-promoting traits (10 to 64%) and biocontrol activity (74% to 82%) against plant pathogens (Xanthomonas and Pseudomonas). This study revealed the high variability in the abundance, diversity, composition, and functionality of endophytic bacteria between ungerminated and germinated seeds in globally commercialized vegetables. Furthermore, potential beneficial endophytic bacteria contained in their seed microbiomes that may contribute to the microbiome of the early stages, development, growth and progeny of vegetables were found.
Collapse
Affiliation(s)
- Jacquelinne J Acuña
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Millennium Institute Center for Genome Regulation (MI-CGR), Valenzuela Puelma 10207, 7800003, Santiago, La Reina, Chile
| | - Jingming Hu
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, 361102, China
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Nitza G Inostroza
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Tamara Valenzuela
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Pablo Perez
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Slava Epstein
- College of Science, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, USA
| | - Angela Sessitsch
- Health & Bioresources, AIT Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430, Tulln, Austria
| | - Qian Zhang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, 361102, China.
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China.
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile.
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile.
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Dundore-Arias JP, Michalska-Smith M, Millican M, Kinkel LL. More Than the Sum of Its Parts: Unlocking the Power of Network Structure for Understanding Organization and Function in Microbiomes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:403-423. [PMID: 37217203 DOI: 10.1146/annurev-phyto-021021-041457] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Plant and soil microbiomes are integral to the health and productivity of plants and ecosystems, yet researchers struggle to identify microbiome characteristics important for providing beneficial outcomes. Network analysis offers a shift in analytical framework beyond "who is present" to the organization or patterns of coexistence between microbes within the microbiome. Because microbial phenotypes are often significantly impacted by coexisting populations, patterns of coexistence within microbiomes are likely to be especially important in predicting functional outcomes. Here, we provide an overview of the how and why of network analysis in microbiome research, highlighting the ways in which network analyses have provided novel insights into microbiome organization and functional capacities, the diverse network roles of different microbial populations, and the eco-evolutionary dynamics of plant and soil microbiomes.
Collapse
Affiliation(s)
- J P Dundore-Arias
- Department of Biology and Chemistry, California State University, Monterey Bay, Seaside, California, USA
| | - M Michalska-Smith
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA;
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | | | - L L Kinkel
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA;
| |
Collapse
|
13
|
Lasa AV, Fernández-González AJ, Villadas PJ, Cobo-Díaz JF, Fernández-López M. Bacterial inoculation of Quercus pyrenaica trees alters co-occurrence patterns but not the composition of the rhizosphere bacteriome in wild conditions. Environ Microbiol 2023; 25:1747-1761. [PMID: 37186411 DOI: 10.1111/1462-2920.16388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 04/18/2023] [Indexed: 05/17/2023]
Abstract
Quercus pyrenaica is a woody species of high landscape value, however, its forests show an advanced state of degradation in the Iberian Peninsula. Afforestation typically has low success, thus, it is necessary to improve the fitness of oaks plantlets to be transplanted, for instance, by inoculating beneficial microorganisms. In adding microorganisms to ecosystems, there must be balanced efficacy with potential effects on native microbial communities. We addressed changes in diversity, richness, composition and co-occurrence networks of prokaryotic communities in the rhizosphere of inoculated and control trees outplanted to three different sites located in the Sierra Nevada National and Natural Park (Spain). After 18 months in wild conditions, we did not detect changes due to the inoculation in the richness, diversity and structure in none of the sites. However, we observed an increase in the complexity of the co-occurrence networks in two experimental areas. Modularization of the networks changed as a result of the inoculation, although the sense of the change depended on the site. Although it was impossible to unravel the effect of bacterial inoculation, our results highlighted that inoculation alters the association of rhizosphere bacteria without entailing other changes, so networks should be analysed prior to inoculating the plantlets.
Collapse
Affiliation(s)
- Ana V Lasa
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | | | - Pablo J Villadas
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, Granada, Spain
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology, Faculty of Veterinary, Universidad de León, León, Spain
| | - M Fernández-López
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, Granada, Spain
| |
Collapse
|
14
|
Abdelfattah A, Tack AJM, Lobato C, Wassermann B, Berg G. From seed to seed: the role of microbial inheritance in the assembly of the plant microbiome. Trends Microbiol 2023; 31:346-355. [PMID: 36481186 DOI: 10.1016/j.tim.2022.10.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 12/10/2022]
Abstract
Despite evidence that the microbiome extends host genetic and phenotypic traits, information on how the microbiome is transmitted and maintained across generations remains fragmented. For seed-bearing plants, seeds harbor a distinct microbiome and play a unique role by linking one generation to the next. Studies on microbial inheritance, a process we suggest including both vertical transmission and the subsequent migration of seed microorganisms to the new plant, thus become essential for our understanding of host evolutionary potential and host-microbiome coevolution. We propose dividing the inheritance process into three stages: (i) plant to seed, (ii) seed dormancy, and (iii) seed to seedling. We discuss the factors affecting the assembly of the microbiome during the three stages, highlight future research directions, and emphasize the implications of microbial inheritance for fundamental science and society.
Collapse
Affiliation(s)
- Ahmed Abdelfattah
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469 Potsdam, Germany; Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden; Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz 8010, Austria.
| | - Ayco J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
| | - Carolina Lobato
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz 8010, Austria
| | - Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz 8010, Austria
| | - Gabriele Berg
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469 Potsdam, Germany; Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz 8010, Austria; Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam OT Golm, Germany
| |
Collapse
|
15
|
Berg G, Schweitzer M, Abdelfattah A, Cernava T, Wassermann B. Missing symbionts – emerging pathogens? Microbiome management for sustainable agriculture. Symbiosis 2023. [DOI: 10.1007/s13199-023-00903-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
AbstractPlant diversification and co-evolution shaped the plant microbiome and vice versa. This resulted in a specific composition of the plant microbiome and a strong connection with the host in terms of functional interplay. Symbionts are part of the microbiota, and important for the plant’s germination and growth, nutrition, as well as stress protection. However, human activities in the Anthropocene are linked to a significant shift of diversity, evenness and specificity of the plant microbiota. In addition, and very importantly, many plant symbionts are missing or no longer functional. It will require targeted microbiome management to support and reintroduce them. In future agriculture, we should aim at replacing harmful chemicals in the field, as well as post-harvest, by using precision microbiome engineering. This is because the plant microbiome is connected across systems and crucial for human and planetary health. This commentary aims to inspire holistic studies for the development of solutions for sustainable agriculture in framework of the One Health and the Planetary Health concepts.
Collapse
|
16
|
Tagele SB, Kim RH, Jeong M, Lim K, Jung DR, Lee D, Kim W, Shin JH. Soil amendment with cow dung modifies the soil nutrition and microbiota to reduce the ginseng replanting problem. FRONTIERS IN PLANT SCIENCE 2023; 14:1072216. [PMID: 36760641 PMCID: PMC9902886 DOI: 10.3389/fpls.2023.1072216] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Ginseng is a profitable crop worldwide; however, the ginseng replanting problem (GRP) is a major threat to its production. Soil amendment is a non-chemical method that is gaining popularity for alleviating continuous cropping obstacles, such as GRP. However, the impact of soil amendment with either cow dung or canola on GRP reduction and the associated soil microbiota remains unclear. In the present study, we evaluated the effect of soil amendment with cow dung, canola seed powder, and without amendment (control), on the survival of ginseng seedling transplants, the soil bacterial and fungal communities, and their associated metabolic functions. The results showed that cow dung increased ginseng seedling survival rate by 100 percent and had a remarkable positive effect on ginseng plant growth compared to control, whereas canola did not. Cow dung improved soil nutritional status in terms of pH, electrical conductivity, NO 3 - , total carbon, total phosphorus, and available phosphorus. The amplicon sequencing results using Illumina MiSeq showed that canola had the strongest negative effect in reducing soil bacterial and fungal diversity. On the other hand, cow dung stimulated beneficial soil microbes, including Bacillus, Rhodanobacter, Streptomyces, and Chaetomium, while suppressing Acidobacteriota. Community-level physiological profiling analysis using Biolog Ecoplates containing 31 different carbon sources showed that cow dung soil had a different metabolic activity with higher utilization rates of carbohydrates and polymer carbon sources, mainly Tween 40 and beta-methyl-d-glucoside. These carbon sources were most highly associated with Bacillota. Furthermore, predicted ecological function analyses of bacterial and fungal communities showed that cow dung had a higher predicted function of fermentation and fewer functions related to plant pathogens and fungal parasites, signifying its potential to enhance soil suppressiveness. Co-occurrence network analysis based on random matrix theory (RMT) revealed that cow dung transformed the soil microbial network into a highly connected and complex network. This study is the first to report the alleviation of GRP using cow dung as a soil amendment, and the study contributes significantly to our understanding of how the soil microbiota and metabolic alterations via cow dung can aid in GRP alleviation.
Collapse
Affiliation(s)
- Setu Bazie Tagele
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- NGS core facility, Kyungpook National University, Daegu, Republic of Korea
| | - Ryeong-Hui Kim
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
| | - Minsoo Jeong
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Kyeongmo Lim
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Da-Ryung Jung
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Dokyung Lee
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
| | - Wanro Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- NGS core facility, Kyungpook National University, Daegu, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Abstract
The seed acts as the primary inoculum source for the plant microbiota. Understanding the processes involved in its assembly and dynamics during germination and seedling emergence has the potential to allow for the improvement of crop establishment. Changes in the bacterial community structure were tracked in 1,000 individual seeds that were collected throughout seed developments of beans and radishes. Seeds were associated with a dominant bacterial taxon that represented more than 75% of all reads. The identity of this taxon was highly variable between the plants and within the seeds of the same plant. We identified selection as the main ecological process governing the succession of dominant taxa during seed filling and maturation. In a second step, we evaluated the seedling transmission of seed-borne taxa in 160 individual plants. While the initial bacterial abundance on seeds was not a good predictor of seedling transmission, the identities of the seed-borne taxa modified the phenotypes of seedlings. Overall, this work revealed that individual seeds are colonized by a few bacterial taxa of highly variable identity, which appears to be important for the early stages of plant development. IMPORTANCE Seeds are key components of plant fitness and are central to the sustainability of the agri-food system. Both the seed quality for food consumption and the seed vigor in agricultural settings can be influenced by the seed microbiota. Understanding the ecological processes involved in seed microbiota assembly will inform future practices for promoting the presence of important seed microorganisms for plant health and productivity. Our results highlighted that seeds were associated with one dominant bacterial taxon of variable taxonomic identity. This variety of dominant taxa was due to (i) spatial heterogeneity between and within plants and (ii) primary succession during seed development. According to neutral models, selection was the main driver of microbial community assembly for both plant species.
Collapse
|
19
|
Zhang Z, Chai X, Gao Y, Zhang B, Lu Y, Du Y, Zhang Y, Ding Y, Tariq A, Ullah A, Li X, Zeng F. Alhagi sparsifolia Harbors a Different Root-Associated Mycobiome during Different Development Stages. Microorganisms 2022; 10:microorganisms10122376. [PMID: 36557629 PMCID: PMC9785364 DOI: 10.3390/microorganisms10122376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/22/2022] [Accepted: 11/26/2022] [Indexed: 12/04/2022] Open
Abstract
The mycobiome in the rhizosphere and within the roots benefits the nutrition and function of host plants. However, compared with the bacterial community, root-associated mycobiomes of desert plants and the forces that drive their assemblage are limited. Here, we investigated the mycobiomes in bulk soil, rhizosphere, and root compartments of Alhagi sparsifolia Shap., a phreatophyte species dominating in Central Asia. The internal transcribed spacer (ITS) gene phylogenetic profiles displayed significantly diverse mycobiomes across three compartments and host growth times, together explaining 31.45% of the variation in the community composition. The community structure of the perennial stage was markedly different from that of other stages (30 days to 2 years old). Along the soil-plant continuum, the α-diversity (estimated by Chao1) decreased gradually, while concomitantly increasing the community dissimilarity and the influence of edaphic factors. Specific leaf area, soil water content, and soil organic matter levels were common factors driving the composition of the three mycobiome communities. A more complex and connected network was observed in the root community compared with the other compartments. Overall, our work suggests that an age-sensitive host effect restructured the desert-plant-root-associated mycobiome, and that edaphic factors and host growth strategy may play potential roles in this process.
Collapse
Affiliation(s)
- Zhihao Zhang
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- Correspondence: (Z.Z.); (F.Z.)
| | - Xutian Chai
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanju Gao
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Zhang
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
| | - Yan Lu
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
| | - Yi Du
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yulin Zhang
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- College of Resource and Environment Sciences, Xinjiang University, Urumqi 830046, China
| | - Ya Ding
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- College of Resource and Environment Sciences, Xinjiang University, Urumqi 830046, China
| | - Akash Tariq
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
| | - Abd Ullah
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangyi Li
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanjiang Zeng
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (Z.Z.); (F.Z.)
| |
Collapse
|
20
|
Yuan YH, Liu LX, Wang L, Dong GZ, Liu YG. Effects of different seasons on bacterial community structure in rose rhizosphere soil. Appl Microbiol Biotechnol 2022; 107:405-417. [DOI: 10.1007/s00253-022-12290-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/31/2022] [Accepted: 11/04/2022] [Indexed: 11/25/2022]
|
21
|
Chandel A, Mann R, Kaur J, Tannenbaum I, Norton S, Edwards J, Spangenberg G, Sawbridge T. Australian native Glycine clandestina seed microbiota hosts a more diverse bacterial community than the domesticated soybean Glycine max. ENVIRONMENTAL MICROBIOME 2022; 17:56. [PMID: 36384698 PMCID: PMC9670509 DOI: 10.1186/s40793-022-00452-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Plant microbiome composition has been demonstrated to change during the domestication of wild plants and it is suggested that this has resulted in loss of plant beneficial microbes. Recently, the seed microbiome of native plants was demonstrated to harbour a more diverse microbiota and shared a common core microbiome with modern cultivars. In this study the composition of the seed-associated bacteria of Glycine clandestina is compared to seed-associated bacteria of Glycine max (soybean). RESULTS The seed microbiome of the native legume Glycine clandestina (crop wild relative; cwr) was more diverse than that of the domesticated Glycine max and was dominated by the bacterial class Gammaproteobacteria. Both the plant species (cwr vs domesticated) and individual seed accessions were identified as the main driver for this diversity and composition of the microbiota of all Glycine seed lots, with the effect of factor "plant species" exceeded that of "geographical location". A core microbiome was identified between the two Glycine species. A high percentage of the Glycine microbiome was unculturable [G. clandestina (80.8%) and G. max (75.5%)] with only bacteria of a high relative abundance being culturable under the conditions of this study. CONCLUSION Our results provided novel insights into the structure and diversity of the native Glycine clandestina seed microbiome and how it compares to that of the domesticated crop Glycine max. Beyond that, it also increased our knowledge of the key microbial taxa associated with the core Glycine spp. microbiome, both wild and domesticated. The investigation of this commonality and diversity is a valuable and essential tool in understanding the use of native Glycine spp. for the discovery of new microbes that would be of benefit to domesticated Glycine max cultivars or any other economically important crops. This study has isolated microbes from a crop wild relative that are now available for testing in G. max for beneficial phenotypes.
Collapse
Affiliation(s)
- Ankush Chandel
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.
| | - Ross Mann
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Jatinder Kaur
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Ian Tannenbaum
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Sally Norton
- Agriculture Victoria Research, Australian Grains Genebank, Horsham, VIC, 3400, Australia
| | - Jacqueline Edwards
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - German Spangenberg
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Timothy Sawbridge
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Rybakova D, Müller H, Olimi E, Schaefer A, Cernava T, Berg G. To defend or to attack? Antagonistic interactions between Serratia plymuthica and fungal plant pathogens, a species-specific volatile dialogue. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.1020634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Volatile organic compounds (VOCs) are involved in microbial interspecies communication and in the mode of action of various antagonistic interactions. They are important for balancing host-microbe interactions and provide the basis for developing biological control strategies to control plant pathogens. We studied the interactions between the bacterial antagonist Serratia plymuthica HRO-C48 and three fungal plant pathogens Rhizoctonia solani, Leptosphaeria maculans and Verticillium longisporum. Significant differences in fungal growth inhibition by the Serratia-emitted VOCs in pairwise dual culture assays and changes in the transcriptome of the bacterium and in the volatilomes of both interacting partners were observed. Even though the rate of fungal growth inhibition by Serratia was variable, the confrontation of the bacterium with the VOCs of all three fungi changed the levels of expression of the genes involved in stress response, biofilm formation, and the production of antimicrobial VOCs. Pairwise interacting microorganisms switched between defense (downregulation of gene expression) and attack (upregulation of gene expression and metabolism followed by growth inhibition of the interacting partner) modes, subject to the combinations of microorganisms that were interacting. In the attack mode HRO-C48 significantly inhibited the growth of R. solani while simultaneously boosting its own metabolism; by contrast, its metabolism was downregulated when HRO-C48 went into a defense mode that was induced by the L. maculans and V. longisporum VOCs. L. maculans growth was slightly reduced by the one bacterial VOC methyl acetate that induced a strong downregulation of expression of genes involved in almost all metabolic functions in S. plymuthica. Similarly, the interaction between S. plymuthica and V. longisporum resulted in an insignificant growth reduction of the fungus and repressed the rate of bacterial metabolism on the transcriptional level, accompanied by an intense volatile dialogue. Overall, our results indicate that VOCs substantially contribute to the highly break species-specific interactions between pathogens and their natural antagonists and thus deserving of increased consideration for pathogen control.
Collapse
|
24
|
Sarenqimuge S, Rahman S, Wang Y, von Tiedemann A. Dormancy and germination of microsclerotia of Verticillium longisporum are regulated by soil bacteria and soil moisture levels but not by nutrients. Front Microbiol 2022; 13:979218. [PMID: 36212810 PMCID: PMC9539216 DOI: 10.3389/fmicb.2022.979218] [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: 06/27/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022] Open
Abstract
The soil-borne pathogen Verticillium longisporum infects roots of its host plant, oilseed rape, and systemically colonizes stems where it finally forms microsclerotia at crop maturity. Once returned to the soil after harvest, microsclerotia undergo a stage of dormancy, in which they may survive for several years. Since there is neither efficient chemical control nor effective resistance in oilseed rape cultivars to control the disease, alternative control strategies may consist in regulating the germination and dormancy of microsclerotia in the soil. Therefore, a series of experiments were conducted to explore the effects of nutrients, soil moisture, and the soil microbiome on germination of dormant microsclerotia. Experiments with microsclerotia exposed in vitro to different nutrients indicated that under sterile conditions the stimulating effect of nutrients on microsclerotia germination was not enhanced as compared to water. Moreover, further assays revealed a strong inhibitory effect of unsterile soil on microsclerotia germination. Accordingly, oilseed rape plants inoculated with microsclerotia of V. longisporum showed severe infection with V. longisporum when grown in autoclaved soil, in contrast to plants grown in unsterile soil. These experiments indicate a crucial role of soil fungistasis and thus the soil microbiome on microsclerotia germination. Further bioassays demonstrated that viable soil bacteria obtained from the rhizosphere of oilseed rape plants and bulk field soil effectively inhibited microsclerotia germination, whereas dead bacteria and bacterial culture filtrates hardly suppressed germination. A putative inhibitory role of volatile organic compounds (VOCs) produced by soil bacteria was confirmed in two-compartment Petri dishes, where microsclerotia germination and colony growth were significantly inhibited. Bacterial VOCs were collected and analyzed by GC–MS. In total, 45 VOCs were identified, among which two acid and two alcohol compounds were emitted by all tested bacteria. A bioassay, conducted with corresponding pure chemicals in two-compartment Petri dishes, indicated that all acidic volatile compounds, including 3-methylbutanoic acid, 2-methylbutanoic acid, hexanoic acid, and 2-methylpropionic acid, induced strong inhibitory effects on microsclerotia. We conclude that bacterial acidic volatiles play a key role in the fungistatic effect on microsclerotia of V. longisporum in the soil and could thus be targeted for development of novel strategies to control this pathogen by artificially regulating dormancy of microsclerotia in soil.
Collapse
Affiliation(s)
- Sarenqimuge Sarenqimuge
- Plant Pathology and Plant Protection Division, Department of Crop Sciences, Faculty of Agriculture, Georg-August University Göttingen, Göttingen, Germany
| | - Shahinoor Rahman
- Agricultural Entomology Division, Department of Crop Sciences, Faculty of Agriculture, Georg-August University Göttingen, Göttingen, Germany
| | - Yao Wang
- Plant Pathology and Plant Protection Division, Department of Crop Sciences, Faculty of Agriculture, Georg-August University Göttingen, Göttingen, Germany
| | - Andreas von Tiedemann
- Plant Pathology and Plant Protection Division, Department of Crop Sciences, Faculty of Agriculture, Georg-August University Göttingen, Göttingen, Germany
- *Correspondence: Andreas von Tiedemann,
| |
Collapse
|
25
|
Qiu Z, Verma JP, Liu H, Wang J, Batista BD, Kaur S, de Araujo Pereira AP, Macdonald CA, Trivedi P, Weaver T, Conaty WC, Tissue DT, Singh BK. Response of the plant core microbiome to Fusarium oxysporum infection and identification of the pathobiome. Environ Microbiol 2022; 24:4652-4669. [PMID: 36059126 DOI: 10.1111/1462-2920.16194] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 09/01/2022] [Indexed: 11/29/2022]
Abstract
Plant core microbiomes consist of persistent key members that provide critical host functions, but their assemblages can be interrupted by biotic and abiotic stresses. The pathobiome is comprised of dynamic microbial interactions in response to disease status of the host. Hence, identifying variation in the core microbiome and pathobiome can significantly advance our understanding of microbial-microbial interactions and consequences for disease progression and host functions. In this study, we combined glasshouse and field studies to analyse the soil and plant rhizosphere microbiome of cotton plants (Gossypium hirsutum) in the presence of a cotton-specific fungal pathogen, Fusarium oxysporum f. sp. vasinfectum (FOV). We found that FOV directly and consistently altered the rhizosphere microbiome, but the biocontrol agents enabled microbial assemblages to resist pathogenic stress. Using co-occurrence network analysis of the core microbiome, we identified the pathobiome comprised of the pathogen and key associate phylotypes in the cotton microbiome. Isolation and application of some negatively correlated pathobiome members provided protection against plant infection. Importantly, our field survey from multiple cotton fields validated the pattern and responses of core microbiomes under FOV infection. This study advances key understanding of core microbiome responses and existence of plant pathobiomes, which provides a novel framework to better manage plant diseases in agriculture and natural settings. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Zhiguang Qiu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Jay Prakash Verma
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Juntao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Bruna D Batista
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Simranjit Kaur
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | | | - Catriona A Macdonald
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Pankaj Trivedi
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Tim Weaver
- CSIRO Agriculture & Food, Locked Bag 59, Narrabri, NSW, Australia
| | - Warren C Conaty
- CSIRO Agriculture & Food, Locked Bag 59, Narrabri, NSW, Australia
| | - David T Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia
| |
Collapse
|
26
|
Ju M, Zhang Q, Wang R, Yan S, Li Z, Li P, Gu P. Correlation in endophytic fungi community diversity and bioactive compounds of Sophora alopecuroides. Front Microbiol 2022; 13:955647. [PMID: 36118208 PMCID: PMC9475766 DOI: 10.3389/fmicb.2022.955647] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 08/04/2022] [Indexed: 12/03/2022] Open
Abstract
Sophora alopecuroides L. is a traditional Chinese medicine used for the treatment of several different disease states including bacillary dysentery and enteritis. But importantly, it also plays a role as an anti-tumor agent. That said, little is known about the role endophytes play regarding the clinically bioactive metabolites in S. alopecuroides. In order to explore the effects of endophytic fungi on the accumulation, quality, and correlation in the content of the medicinal compounds, the structural diversity of endophytic fungi in S. alopecuroides was analyzed. The relationship between endophytes and quinolizidine alkaloids (QAs), housed within the seeds of S. alopecuroides, which were interpreted based on established methods of high-throughput sequencing and high-performance liquid chromatography. A total of 1,034,418 effective sequence reads and 257 operational taxonomic units (OTUs) were obtained from 33 samples which were sourced from 11 different sampling sites and further classified into 9 phyla, 20 classes, 45 orders, 85 families, and 118 genera. Ascomycota was found to be the dominant phylum of endophytic fungi in S. alopecuroides, with a relative abundance ranging from 60.85 to 98.30%. Alternaria, Cladosporium, Filobasidium, and an unidentified Ascomycota were the core-shared endophytes, accounting for 49.96, 27.12, 14.83, and 7.88%, respectively. Correlation analysis showed that the Simpson's diversity index of endophytic fungal community in S. alopecuroides was significantly positively correlated with the Oxymatrine (OMA) content in different areas, while the Chao and Shannoneven indexes were significantly negatively correlated with OMA. The endophytic fungi of Alternaria were positively correlated with the content of OMA, Oxysophocarpine (OSC), and total QAs. This study has mastered the endophytic fungi resources of S. alopecuroides, explored potential functional endophytic fungi, and provided a scientific basis for using biological fertilization strategies to improve the quality of S. alopecuroides.
Collapse
Affiliation(s)
- Mingxiu Ju
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Qingchen Zhang
- Department of Pharmacotherapy and Translational Research, University of Florida, Gainesville, FL, United States
| | - Ruotong Wang
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Siyuan Yan
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Zhengnan Li
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, China
| | - Peng Li
- State Key Laboratory of High-Efficiency Utilization of Coal and Green Chemical Engineering, Ningxia University, Yinchuan, China
| | - Peiwen Gu
- School of Agriculture, Ningxia University, Yinchuan, China
| |
Collapse
|
27
|
Three semi-selective media for Pseudomonas syringae pv. maculicola and P. cannabina pv. alisalensis. Appl Microbiol Biotechnol 2022; 106:5741-5755. [PMID: 35930039 DOI: 10.1007/s00253-022-12092-w] [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: 02/18/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 11/02/2022]
Abstract
Three semi-selective media, DTarTA, SPbc, and SPamt, were developed and tested to isolate Pseudomonas syringae pv. maculicola (Psm) and P. cannabina pv. alisalensis (Pca) from Raphanus sativus seeds. DTarTA contained D-tartaric acid as a carbon source and potassium tellurite, ampicillin sodium, and methyl violet as antibiotics. DTarTA suppressed growth in 19 of the 24 pathovars from the P. syringae complex, whereas Psm and Pca grew and formed gray to black colonies. SPamt contained sucrose and peptone as nutrient sources and was supplemented with bromothymol blue and the same antibiotics present in DTarTA and Psm and Pca formed yellowish to dark brown colonies on the SPamt medium. SPbc contained sucrose and peptone and was supplemented with cephalexin and boric acid as antibiotics and Psm and Pca formed semi-translucent to white colonies on the SPbc medium. SPamt and SPbc suppressed the growth of several plant-associated bacteria (except the P. syringae complex). The growth of saprophytic bacteria in seeds on the different media was compared with that on King's B medium, using five types of commercially available Raphanus sativus seeds. The suppression rate of DTarTA was 85-99% and was lower for seeds with more saprophytic bacteria. The suppression rates of SPamt and SPbc were 90-99%. In detection tests using 10,000 seed samples mixed with Pca or Psm-contaminated seeds, it was possible to selectively isolate Psm and Pca using SPamt and SPbc, even when the colony numbers of the target bacterium constituted less than 10% of the total colonies. KEY POINTS: • Bacterial leaf spot and blight pathogens were selectively isolated from seeds. • DTarTA medium distinguishes these pathogens from P. syringae complex pathovars. • SPamp and SPbc media have different selectivity for plant-associated bacteria.
Collapse
|
28
|
Stimulation of Distinct Rhizosphere Bacteria Drives Phosphorus and Nitrogen Mineralization in Oilseed Rape under Field Conditions. mSystems 2022; 7:e0002522. [PMID: 35862821 PMCID: PMC9426549 DOI: 10.1128/msystems.00025-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Advances in DNA sequencing technologies have drastically changed our perception of the structure and complexity of the plant microbiome. By comparison, our ability to accurately identify the metabolically active fraction of soil microbiota and its specific functional role in augmenting plant health is relatively limited. Important ecological interactions being performed by microbes can be investigated by analyzing the extracellular protein fraction. Here, we combined a unique protein extraction method and an iterative bioinformatics pipeline to capture and identify extracellular proteins (metaexoproteomics) synthesized in the rhizosphere of Brassica spp. We first validated our method in the laboratory by successfully identifying proteins related to a host plant (Brassica rapa) and its bacterial inoculant, Pseudomonas putida BIRD-1. This identified numerous rhizosphere specific proteins linked to the acquisition of plant-derived nutrients in P. putida. Next, we analyzed natural field-soil microbial communities associated with Brassica napus L. (oilseed rape). By combining metagenomics with metaexoproteomics, 1,885 plant, insect, and microbial proteins were identified across bulk and rhizosphere samples. Metaexoproteomics identified a significant shift in the metabolically active fraction of the soil microbiota responding to the presence of B. napus roots that was not apparent in the composition of the total microbial community (metagenome). This included stimulation of rhizosphere-specialized bacteria, such as Gammaproteobacteria, Betaproteobacteria, and Flavobacteriia, and the upregulation of plant beneficial functions related to phosphorus and nitrogen mineralization. Our metaproteomic assessment of the “active” plant microbiome at the field-scale demonstrates the importance of moving beyond metagenomics to determine ecologically important plant-microbe interactions underpinning plant health. IMPORTANCE Plant-microbe interactions are critical to ecosystem function and crop production. While significant advances have been made toward understanding the structure of the plant microbiome, learning about its full functional role is still in its infancy. This is primarily due to an incomplete ability to determine in situ plant-microbe interactions actively operating under field conditions. Proteins are the functional entities of the cell. Therefore, their identification and relative quantification within a microbial community provide the best proxy for which microbes are the most metabolically active and which are driving important plant-microbe interactions. Here, we provide the first metaexoproteomics assessment of the plant microbiome using field-grown oilseed rape as the model crop species, identifying key taxa responsible for specific ecological interactions. Gaining a mechanistic understanding of the plant microbiome is central to developing engineered plant microbiomes to improve sustainable agricultural approaches and reduce our reliance on nonrenewable resources.
Collapse
|
29
|
Medina-Paz F, Herrera-Estrella L, Heil M. All Set before Flowering: A 16S Gene Amplicon-Based Analysis of the Root Microbiome Recruited by Common Bean ( Phaseolus vulgaris) in Its Centre of Domestication. PLANTS (BASEL, SWITZERLAND) 2022; 11:1631. [PMID: 35807585 PMCID: PMC9269403 DOI: 10.3390/plants11131631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/18/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Plant roots recruit most prokaryotic members of their root microbiota from the locally available inoculum, but knowledge on the contribution of native microorganisms to the root microbiota of crops in native versus non-native areas remains scarce. We grew common bean (Phaseolus vulgaris) at a field site in its centre of domestication to characterise rhizosphere and endosphere bacterial communities at the vegetative, flowering, and pod filling stage. 16S r RNA gene amplicon sequencing of ten samples yielded 9,401,757 reads, of which 8,344,070 were assigned to 17,352 operational taxonomic units (OTUs). Rhizosphere communities were four times more diverse than in the endosphere and dominated by Actinobacteria, Bacteroidetes, Crenarchaeota, and Proteobacteria (endosphere: 99% Proteobacteria). We also detected high abundances of Gemmatimonadetes (6%), Chloroflexi (4%), and the archaeal phylum Thaumarchaeota (Candidatus Nitrososphaera: 11.5%): taxa less frequently reported from common bean rhizosphere. Among 154 OTUs with different abundances between vegetative and flowering stage, we detected increased read numbers of Chryseobacterium in the endosphere and a 40-fold increase in the abundances of OTUs classified as Rhizobium and Aeromonas (equivalent to 1.5% and over 6% of all reads in the rhizosphere). Our results indicate that bean recruits specific taxa into its microbiome when growing 'at home'.
Collapse
Affiliation(s)
- Francisco Medina-Paz
- Laboratorio de Ecología de Plantas, Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados (CINVESTAV)—Unidad Irapuato, Irapuato 36824, GTO, Mexico;
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados (CINVESTAV)—Unidad de Genómica Avanzada, Irapuato 36824, GTO, Mexico; or
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79424, USA
| | - Martin Heil
- Laboratorio de Ecología de Plantas, Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados (CINVESTAV)—Unidad Irapuato, Irapuato 36824, GTO, Mexico;
| |
Collapse
|
30
|
Hafiz FB, Moradtalab N, Goertz S, Rietz S, Dietel K, Rozhon W, Humbeck K, Geistlinger J, Neumann G, Schellenberg I. Synergistic Effects of a Root-Endophytic Trichoderma Fungus and Bacillus on Early Root Colonization and Defense Activation Against Verticillium longisporum in Rapeseed. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:380-392. [PMID: 35147443 DOI: 10.1094/mpmi-11-21-0274-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Rhizosphere-competent microbes often interact with plant roots and exhibit beneficial effects on plant performance. Numerous bacterial and fungal isolates are able to prime host plants for fast adaptive responses against pathogen attacks. Combined action of fungi and bacteria may lead to synergisms exceeding effects of single strains. Individual beneficial fungi and bacteria have been extensively studied in Arabidopsis thaliana, but little is known about their concerted actions in the Brassicaceae. Here, an in-vitro system with oilseed rape (Brassica napus) was established. Roots of two different cultivars were inoculated with well-characterized fungal (Trichoderma harzianum OMG16) and bacterial (Bacillus velezensis FZB42) isolates alone or in combination. Microscopic analysis confirmed that OMG16 hyphae entered root hairs through root hair tips and formed distinct intracellular structures. Quantitative PCR revealed that root colonization of OMG16 increased up to 10-fold in the presence of FZB42. Relative transcript levels of the ethylene- and jasmonic acid-responsive genes PDF1.2, ERF2, and AOC3 were recorded in leaves by quantitative reverse transcription PCR to measure induced systemic resistance in tissues distant from the roots. Combined action of OMG16 and FZB42 induced transcript abundances more efficiently than single inoculation. Importantly, microbial priming reduced Verticillium longisporum root infection in rapeseed by approximately 100-fold compared with nonprimed plants. Priming also led to faster and stronger systemic responses of the defense genes PDF1.2, ERF2, AOC3, and VSP2.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Fatema Binte Hafiz
- Department of Agriculture, Ecotrophology, and Landscape Development, Anhalt University of Applied Sciences, 06406 Bernburg, Saxony-Anhalt, Germany
| | - Narges Moradtalab
- Institute of Crop Sciences, University of Hohenheim, 70593 Stuttgart, Baden-Württemberg, Germany
| | - Simon Goertz
- NPZ Innovation GmbH, Hohenlieth-Hof, 24363, Holtsee, Schleswig-Holstein, Germany
| | - Steffen Rietz
- NPZ Innovation GmbH, Hohenlieth-Hof, 24363, Holtsee, Schleswig-Holstein, Germany
| | | | - Wilfried Rozhon
- Department of Agriculture, Ecotrophology, and Landscape Development, Anhalt University of Applied Sciences, 06406 Bernburg, Saxony-Anhalt, Germany
| | - Klaus Humbeck
- Institute of Biology, Plant Physiology Department, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Saxony-Anhalt, Germany
| | - Joerg Geistlinger
- Department of Agriculture, Ecotrophology, and Landscape Development, Anhalt University of Applied Sciences, 06406 Bernburg, Saxony-Anhalt, Germany
| | - Günter Neumann
- Institute of Crop Sciences, University of Hohenheim, 70593 Stuttgart, Baden-Württemberg, Germany
| | - Ingo Schellenberg
- Department of Agriculture, Ecotrophology, and Landscape Development, Anhalt University of Applied Sciences, 06406 Bernburg, Saxony-Anhalt, Germany
| |
Collapse
|
31
|
Simonin M, Briand M, Chesneau G, Rochefort A, Marais C, Sarniguet A, Barret M. Seed microbiota revealed by a large-scale meta-analysis including 50 plant species. THE NEW PHYTOLOGIST 2022; 234:1448-1463. [PMID: 35175621 DOI: 10.1111/nph.18037] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/03/2022] [Indexed: 05/15/2023]
Abstract
Seed microbiota constitutes a primary inoculum for plants that is gaining attention owing to its role for plant health and productivity. Here, we performed a meta-analysis on 63 seed microbiota studies covering 50 plant species to synthesize knowledge on the diversity of this habitat. Seed microbiota are diverse and extremely variable, with taxa richness varying from one to thousands of taxa. Hence, seed microbiota presents a variable (i.e. flexible) microbial fraction but we also identified a stable (i.e. core) fraction across samples. Around 30 bacterial and fungal taxa are present in most plant species and in samples from all over the world. Core taxa, such as Pantoea agglomerans, Pseudomonas viridiflava, P. fluorescens, Cladosporium perangustum and Alternaria sp., are dominant seed taxa. The characterization of the core and flexible seed microbiota provided here will help uncover seed microbiota roles for plant health and design effective microbiome engineering.
Collapse
Affiliation(s)
- Marie Simonin
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d'Angers, F-49000, Angers, France
| | - Martial Briand
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d'Angers, F-49000, Angers, France
| | - Guillaume Chesneau
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d'Angers, F-49000, Angers, France
| | - Aude Rochefort
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d'Angers, F-49000, Angers, France
| | - Coralie Marais
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d'Angers, F-49000, Angers, France
| | - Alain Sarniguet
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d'Angers, F-49000, Angers, France
| | - Matthieu Barret
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d'Angers, F-49000, Angers, France
| |
Collapse
|
32
|
Struck C, Rüsch S, Strehlow B. Control Strategies of Clubroot Disease Caused by Plasmodiophora brassicae. Microorganisms 2022; 10:620. [PMID: 35336194 PMCID: PMC8949847 DOI: 10.3390/microorganisms10030620] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/17/2022] [Accepted: 03/11/2022] [Indexed: 12/04/2022] Open
Abstract
The clubroot disease caused by the soil-borne pathogen Plasmodiophora brassicae is one of the most important diseases of cruciferous crops worldwide. As with many plant pathogens, the spread is closely related to the cultivation of suitable host plants. In addition, temperature and water availability are crucial determinants for the occurrence and reproduction of clubroot disease. Current global changes are contributing to the widespread incidence of clubroot disease. On the one hand, global trade and high prices are leading to an increase in the cultivation of the host plant rapeseed worldwide. On the other hand, climate change is improving the living conditions of the pathogen P. brassicae in temperate climates and leading to its increased occurrence. Well-known ways to control efficiently this disease include arable farming strategies: growing host plants in wide crop rotations, liming the contaminated soils, and using resistant host plants. Since chemical control of the clubroot disease is not possible or not ecologically compatible, more and more alternative control options are being investigated. In this review, we address the challenges for its control, with a focus on biological control options.
Collapse
Affiliation(s)
- Christine Struck
- Faculty of Agricultural and Environmental Sciences, University of Rostock, Satower Str. 48, 18059 Rostock, Germany;
| | - Stefanie Rüsch
- Faculty of Agricultural and Environmental Sciences, University of Rostock, Satower Str. 48, 18059 Rostock, Germany;
| | - Becke Strehlow
- Faculty of Agriculture and Food Sciences, University of Applied Sciences Neubrandenburg, Brodaer Str. 2, 17033 Neubrandenburg, Germany;
| |
Collapse
|
33
|
Padeniya U, Larson ET, Septriani S, Pataueg A, Kafui AR, Hasan E, Mmaduakonam OS, Kim GD, Kiddane AT, Brown CL. Probiotic Treatment Enhances Pre-feeding Larval Development and Early Survival in Zebrafish Danio rerio. JOURNAL OF AQUATIC ANIMAL HEALTH 2022; 34:3-11. [PMID: 35315145 DOI: 10.1002/aah.10148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 12/03/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
The growth and development of healthy culture subjects are essential in increasing productivity in the aquaculture industry. A primary determinant of aquatic animal productivity is the ambient microbial population. If an aquatic animal's microbiome is diverse, with bacteria favoring beneficial over pathogenic species, the health and growth of the animal (i.e., fish or crustacean) can be substantially improved. Embryonic and newly hatched Zebrafish Danio rerio larvae were reared in the presence of (1) water from the broodstock culture tank as a control, (2) a probiotic solution containing 19 strains of live lactic acid bacteria (LAB), or (3) an antibiotic (AB) solution with amoxycillin. Developmental parameters were monitored until 10 d postfertilization. Bacteria present in the water and larvae were cultured and identified by sequencing the V4 hypervariable region of bacterial 16S ribosomal RNA. Probiotic-treated larvae showed significant increases in every measured morphological parameter and in survival compared to the controls and AB-treated larvae, including TL, eye development, and swim bladder development before first feeding. Staining with DASPEI (2-(4-[dimethylamino]styryl)-N-ethylpyridinium iodide) produced fluorescence, revealing increased mitochondrial activity in the gastrointestinal tracts of probiotic-treated larvae and reflecting advancement of initial metabolic function. Probiotic-treated larvae showed accelerated yolk absorption, resulting in increased nutrient mobilization and growth. Microbial analyses revealed a greater concentration of bacteria in larvae in response to the probiotic treatment compared to the other two treatments. Species identified in all three treatments included Pseudomonas spp. and Aeromonas spp. (Proteobacteria). The second most diverse and abundant microbiome was seen in controls, whereas AB-treated larvae had the least diverse microbiome. All treatments revealed the presence of proteobacteria, but an AB-resistant pathogenic bacterium (Stenotrophomonas maltophilia) was identified in the AB group. These results reveal that the presence of LAB and other bacteria favorably influenced early larval growth, development, digestive function, and survival in Zebrafish even before the onset of feeding.
Collapse
Affiliation(s)
- Uthpala Padeniya
- Food and Agriculture Organization of the United Nations, World Fisheries University Pilot Programme, Pukyong National University, Busan, 48547, South Korea
| | - Earl T Larson
- Department of Biological Sciences, St. Johns River State College, Orange Park, Florida, 32065, USA
| | - Shafira Septriani
- Food and Agriculture Organization of the United Nations, World Fisheries University Pilot Programme, Pukyong National University, Busan, 48547, South Korea
| | - Arjay Pataueg
- Food and Agriculture Organization of the United Nations, World Fisheries University Pilot Programme, Pukyong National University, Busan, 48547, South Korea
| | - Akpoh Rhoda Kafui
- Food and Agriculture Organization of the United Nations, World Fisheries University Pilot Programme, Pukyong National University, Busan, 48547, South Korea
| | - Ekramul Hasan
- Food and Agriculture Organization of the United Nations, World Fisheries University Pilot Programme, Pukyong National University, Busan, 48547, South Korea
| | - Obodoefuna Somadina Mmaduakonam
- Food and Agriculture Organization of the United Nations, World Fisheries University Pilot Programme, Pukyong National University, Busan, 48547, South Korea
| | - Gun-Do Kim
- Lab of Cell Signaling, Department of Microbiology, College of Natural Science, Pukyong National University, Busan, 48547, South Korea
| | - Anley Teferra Kiddane
- Lab of Cell Signaling, Department of Microbiology, College of Natural Science, Pukyong National University, Busan, 48547, South Korea
| | - Christopher L Brown
- Food and Agriculture Organization of the United Nations, World Fisheries University Pilot Programme, Pukyong National University, Busan, 48547, South Korea
| |
Collapse
|
34
|
Liu D, Cai J, He H, Yang S, Chater CCC, Yu F. Anemochore Seeds Harbor Distinct Fungal and Bacterial Abundance, Composition, and Functional Profiles. J Fungi (Basel) 2022; 8:89. [PMID: 35050030 PMCID: PMC8778408 DOI: 10.3390/jof8010089] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 02/01/2023] Open
Abstract
Many plants adapted to harsh environments have evolved low seed mass ('light seeds') with specific dispersal strategies, primarily either by wind (anemochory) or water (hydrochory). However, the role of their seed microbiota in their survival, and their seed microbial abundance and structure, remain insufficiently studied. Herein, we studied the light seed microbiome of eight anemochores and two hydrochores (as controls) collected from four provinces in China, using qPCR and metagenomic sequencing targeting both bacteria and fungi. Substantial variations were found for seed endophytic fungi (9.9 × 1010~7.3 × 102 gene copy numbers per seed) and bacteria (1.7 × 1010~8.0 × 106). Seed microbial diversity and structure were mainly driven by the plant genotype (species), with weak influences from their host plant classification level or dispersal mode. Seed microbial composition differences were clear at the microbial phylum level, with dominant proportions (~75%) for Proteobacteria and Ascomycota. The light seeds studied harbored unique microbial signatures, sharing only two Halomonas amplicon sequence variants (ASVs) and two fungal ASVs affiliated to Alternaria and Cladosporium. A genome-level functional profile analysis revealed that seed bacterial microbiota were enriched in amino acid, nucleoside, and nucleotide biosynthesis, while in fungal communities the generation of precursor metabolites and respiration were more highly represented. Together, these novel insights provide a deeper understanding of highly diversified plant-specific light seed microbiota and ecological strategies for plants in harsh environments.
Collapse
Affiliation(s)
- Dong Liu
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.C.); (H.H.); (S.Y.)
| | - Jie Cai
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.C.); (H.H.); (S.Y.)
| | - Huajie He
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.C.); (H.H.); (S.Y.)
| | - Shimei Yang
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.C.); (H.H.); (S.Y.)
| | | | - Fuqiang Yu
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.C.); (H.H.); (S.Y.)
| |
Collapse
|
35
|
Abdullaeva Y, Ratering S, Ambika Manirajan B, Rosado-Porto D, Schnell S, Cardinale M. Domestication Impacts the Wheat-Associated Microbiota and the Rhizosphere Colonization by Seed- and Soil-Originated Microbiomes, Across Different Fields. FRONTIERS IN PLANT SCIENCE 2022; 12:806915. [PMID: 35095978 PMCID: PMC8789879 DOI: 10.3389/fpls.2021.806915] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/13/2021] [Indexed: 05/17/2023]
Abstract
The seed-transmitted microorganisms and the microbiome of the soil in which the plant grows are major drivers of the rhizosphere microbiome, a crucial component of the plant holobiont. The seed-borne microbiome can be even coevolved with the host plant as a result of adaptation and vertical transmission over generations. The reduced genome diversity and crossing events during domestication might have influenced plant traits that are important for root colonization by seed-borne microbes and also rhizosphere recruitment of microbes from the bulk soil. However, the impact of the breeding on seed-transmitted microbiome composition and the plant ability of microbiome selection from the soil remain unknown. Here, we analyzed both endorhiza and rhizosphere microbiome of two couples of genetically related wild and cultivated wheat species (Aegilops tauschii/Triticum aestivum and T. dicoccoides/T. durum) grown in three locations, using 16S rRNA gene and ITS2 metabarcoding, to assess the relative contribution of seed-borne and soil-derived microbes to the assemblage of the rhizosphere microbiome. We found that more bacterial and fungal ASVs are transmitted from seed to the endosphere of all species compared with the rhizosphere, and these transmitted ASVs were species-specific regardless of location. Only in one location, more microbial seed transmission occurred also in the rhizosphere of A. tauschii compared with other species. Concerning soil-derived microbiome, the most distinct microbial genera occurred in the rhizosphere of A. tauschii compared with other species in all locations. The rhizosphere of genetically connected wheat species was enriched with similar taxa, differently between locations. Our results demonstrate that host plant criteria for soil bank's and seed-originated microbiome recruitment depend on both plants' genotype and availability of microorganisms in a particular environment. This study also provides indications of coevolution between the host plant and its associated microbiome resulting from the vertical transmission of seed-originated taxa.
Collapse
Affiliation(s)
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | | | - David Rosado-Porto
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | - Massimiliano Cardinale
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
- Department of Biological and Environmental Sciences and Technologies – DiSTeBA, University of Salento, Lecce, Italy
| |
Collapse
|
36
|
Moreira ZPM, Helgason BL, Germida JJ. Assembly and potential transmission of the lens culinaris seed microbiome. FEMS Microbiol Ecol 2021; 97:6484792. [PMID: 34958355 DOI: 10.1093/femsec/fiab166] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/22/2021] [Indexed: 11/12/2022] Open
Abstract
Soil is an important source of bacteria and fungi for the plant, but seeds can also provide microbial inocula through heritable or stochastic assembly. Seed-associated microbial communities can potentially interact with the host plant through multiple generations. Here, we assessed the impact of two different soil types on the seed microbiome assembly of seven lentil (Lens culinaris) genotypes under environmentally controlled conditions and examined the vertical transmission of bacterial communities from seed to seed across two generations. Bulk soil microbiomes and seed microbiomes were characterized using high-throughput amplicon sequencing of the bacterial 16S rRNA gene. Our results revealed that bacterial communities in the two soils differed significantly and that bacterial communities associated with seeds were significantly impacted by genotype (15%) in one of the soils. Co-occurrence of amplicon sequence variants (ASVs) between generations suggests members of the genera Cutibacterium, Methylobacterium, Sphingomonas, Streptococcus, and Tepidimonas are transmitted and preserved in lentil genotypes irrespective of the soil in which they were grown. Increasing our knowledge of how microbial communities carried by seeds are assembled, transmitted, and preserved offers a promising way for future breeding programs to consider microbial communities when selecting for more resilient and productive cultivars.
Collapse
Affiliation(s)
- Zayda P Morales Moreira
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Bobbi L Helgason
- Department of Soil Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - James J Germida
- Department of Soil Science, University of Saskatchewan, Saskatoon, SK, Canada
| |
Collapse
|
37
|
Chandel A, Mann R, Kaur J, Norton S, Edwards J, Spangenberg G, Sawbridge T. Implications of Seed Vault Storage Strategies for Conservation of Seed Bacterial Microbiomes. Front Microbiol 2021; 12:784796. [PMID: 34925291 PMCID: PMC8678515 DOI: 10.3389/fmicb.2021.784796] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 10/25/2021] [Indexed: 12/20/2022] Open
Abstract
Global seed vaults are important, as they conserve plant genetic resources for future breeding to improve crop yield and quality and to overcome biotic and abiotic stresses. However, little is known about the impact of standard storage procedures, such as seed drying and cold storage on the seed bacterial community, and the ability to recover seed-associated bacteria after storage. In this study, soybean [Glycine max (L.) Merr.] seeds were analyzed to characterize changes in the bacterial community composition and culturability under varying storage conditions. The G. max bacterial microbiome was analyzed from undried seed, dried seed, and seed stored for 0, 3, 6, and 14months. Storage temperatures consisted of -20°C, 4°C, and room temperature (RT), with -20°C being commonly used in seed storage vaults globally. The seed microbiome of G. max was dominated by Gammaproteobacteria under all conditions. Undried seed was dominated by Pantoea (33.9%) and Pseudomonas (51.1%); however, following drying, the abundance of Pseudomonas declined significantly (0.9%), Pantoea increased significantly (73.6%), and four genera previously identified including Pajaroellobacter, Nesterenkonia, env.OPS_17, and Acidibacter were undetectable. Subsequent storage at RT, 4, or -20°C maintained high-abundance Genera at the majority of time points, although RT caused greater fluctuations in abundances. For many of the low-abundance Genera, storage at -20°C resulted in their gradual disappearance, whereas storage at 4°C or RT resulted in their more rapid disappearance. The changes in seed bacterial composition were reflected by cultured bacterial taxa obtained from the stored G. max seed. The main taxa were largely culturable and had similar relative abundance, while many, but not all, of the low-abundance taxa were also culturable. Overall, these results indicate that the initial seed drying affects the seed bacterial composition, suggesting that microbial isolation prior to seed drying is recommended to conserve these microbes. The standard seed storage condition of -20°C is most suitable for conservation of the bacterial seed microbiome, as this storage temperature slows down the loss of seed bacterial diversity over longer time periods, particularly low-abundance taxa.
Collapse
Affiliation(s)
- Ankush Chandel
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Ross Mann
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Jatinder Kaur
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Sally Norton
- Agriculture Victoria Research, Australian Grains Genebank, Horsham, VIC, Australia
| | - Jacqueline Edwards
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - German Spangenberg
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Timothy Sawbridge
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| |
Collapse
|
38
|
Bziuk N, Maccario L, Straube B, Wehner G, Sørensen SJ, Schikora A, Smalla K. The treasure inside barley seeds: microbial diversity and plant beneficial bacteria. ENVIRONMENTAL MICROBIOME 2021; 16:20. [PMID: 34711269 PMCID: PMC8554914 DOI: 10.1186/s40793-021-00389-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/04/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND Bacteria associated with plants can enhance the plants' growth and resistance against phytopathogens. Today, growers aim to reduce the use of mineral fertilizers and pesticides. Since phytopathogens cause severe yield losses in crop production systems, biological alternatives gain more attention. Plant and also seed endophytes have the potential to influence the plant, especially seed-borne bacteria may express their beneficiary impact at initial plant developmental stages. In the current study, we assessed the endophytic seed microbiome of seven genetically diverse barley accessions by 16S rRNA gene amplicon sequencing and verified the in vitro plant beneficial potential of isolated seed endophytes. Furthermore, we investigated the impact of the barley genotype and its seed microbiome on the rhizosphere microbiome at an early growth stage by 16S rRNA gene amplicon sequencing. RESULTS The plant genotype displayed a significant impact on the microbiota in both barley seed and rhizosphere. Consequently, the microbial alpha- and beta-diversity of the endophytic seed microbiome was highly influenced by the genotype. Interestingly, no correlation was observed between the endophytic seed microbiome and the single nucleotide polymorphisms of the seven genotypes. Unclassified members of Enterobacteriaceae were by far most dominant. Other abundant genera in the seed microbiome belonged to Curtobacterium, Paenibacillus, Pantoea, Sanguibacter and Saccharibacillus. Endophytes isolated from barley seeds were affiliated to dominant genera of the core seed microbiome, based on their 16S rRNA gene sequence. Most of these endophytic isolates produced in vitro plant beneficial secondary metabolites known to induce plant resistance. CONCLUSION Although barley accessions representing high genetic diversity displayed a genotype-dependent endophytic seed microbiome, a core seed microbiome with high relative abundances was identified. Endophytic isolates were affiliated to members of the core seed microbiome and many of them showed plant beneficial properties. We propose therefore that new breeding strategies should consider genotypes with high abundance of beneficial microbes.
Collapse
Affiliation(s)
- Nina Bziuk
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Lorrie Maccario
- Section of Microbiology, Copenhagen University, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Benjamin Straube
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Gwendolin Wehner
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Søren J. Sørensen
- Section of Microbiology, Copenhagen University, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Adam Schikora
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Messeweg 11-12, 38104 Braunschweig, Germany
| |
Collapse
|
39
|
de Medeiros Azevedo T, Aburjaile FF, Ferreira-Neto JRC, Pandolfi V, Benko-Iseppon AM. The endophytome (plant-associated microbiome): methodological approaches, biological aspects, and biotech applications. World J Microbiol Biotechnol 2021; 37:206. [PMID: 34708327 DOI: 10.1007/s11274-021-03168-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/05/2021] [Indexed: 11/25/2022]
Abstract
Similar to other organisms, plants establish interactions with a variety of microorganisms in their natural environment. The plant microbiome occupies the host plant's tissues, either internally or on its surfaces, showing interactions that can assist in its growth, development, and adaptation to face environmental stresses. The advance of metagenomics and metatranscriptomics approaches has strongly driven the study and recognition of plant microbiome impacts. Research in this regard provides comprehensive information about the taxonomic and functional aspects of microbial plant communities, contributing to a better understanding of their dynamics. Evidence of the plant microbiome's functional potential has boosted its exploitation to develop more ecological and sustainable agricultural practices that impact human health. Although microbial inoculants' development and use are promising to revolutionize crop production, interdisciplinary studies are needed to identify new candidates and promote effective practical applications. On the other hand, there are challenges in understanding and analyzing complex data generated within a plant microbiome project's scope. This review presents aspects about the complex structuring and assembly of the microbiome in the host plant's tissues, metagenomics, and metatranscriptomics approaches for its understanding, covering descriptions of recent studies concerning metagenomics to characterize the microbiome of non-model plants under different aspects. Studies involving bio-inoculants, isolated from plant microbial communities, capable of assisting in crops' productivity, are also reviewed.
Collapse
Affiliation(s)
- Thamara de Medeiros Azevedo
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - Flávia Figueira Aburjaile
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - José Ribamar Costa Ferreira-Neto
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - Valesca Pandolfi
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - Ana Maria Benko-Iseppon
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil.
| |
Collapse
|
40
|
Fernández-González AJ, Ramírez-Tejero JA, Nevado-Berzosa MP, Luque F, Fernández-López M, Mercado-Blanco J. Coupling the endophytic microbiome with the host transcriptome in olive roots. Comput Struct Biotechnol J 2021; 19:4777-4789. [PMID: 34504670 PMCID: PMC8411203 DOI: 10.1016/j.csbj.2021.08.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/06/2021] [Accepted: 08/20/2021] [Indexed: 12/13/2022] Open
Abstract
The connection between olive genetic responses to environmental and agro-climatic conditions and the composition, structure and functioning of host-associated, belowground microbiota has never been studied under the holobiont conceptual framework. Two groups of cultivars growing under the same environmental, pedological and agronomic conditions, and showing highest (AH) and lowest (AL) Actinophytocola relative abundances, were earlier identified. We aimed now to: i) compare the root transcriptome profiles of these two groups harboring significantly different relative abundances in the above-mentioned bacterial genus; ii) examine their rhizosphere and root-endosphere microbiota co-occurrence networks; and iii) connect the root host transcriptome pattern to the composition of the root microbial communities by correlation and co-occurrence network analyses. Significant differences in olive gene expression were found between the two groups. Co-occurrence networks of the root endosphere microbiota were clearly different as well. Pearson's correlation analysis enabled a first portray of the interaction occurring between the root host transcriptome and the endophytic community. To further identify keystone operational taxonomic units (OTUs) and genes, subsequent co-occurrence network analysis showed significant interactions between 32 differentially expressed genes (DEGs) and 19 OTUs. Overall, negative correlation was detected between all upregulated genes in the AH group and all OTUs except of Actinophytocola. While two groups of olive cultivars grown under the same conditions showed significantly different microbial profiles, the most remarkable finding was to unveil a strong correlation between these profiles and the differential gene expression pattern of each group. In conclusion, this study shows a holistic view of the plant-microbiome communication.
Collapse
Affiliation(s)
- Antonio J. Fernández-González
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Calle Profesor Albareda 1, 18008 Granada, Spain
| | - Jorge A. Ramírez-Tejero
- Departamento de Biología Experimental, Centro de Estudios Avanzados en Olivar y Aceites de Oliva, Universidad de Jaén, Jaén 23071, Spain
| | - María Patricia Nevado-Berzosa
- Departamento de Biología Experimental, Centro de Estudios Avanzados en Olivar y Aceites de Oliva, Universidad de Jaén, Jaén 23071, Spain
| | - Francisco Luque
- Departamento de Biología Experimental, Centro de Estudios Avanzados en Olivar y Aceites de Oliva, Universidad de Jaén, Jaén 23071, Spain
| | - Manuel Fernández-López
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Calle Profesor Albareda 1, 18008 Granada, Spain
| | - Jesús Mercado-Blanco
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, CSIC, Campus ‘Alameda del Obispo’ s/n, Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain
| |
Collapse
|
41
|
Liang D, Guo J, Hou F, Bowatte S. High level of conservation and diversity among the endophytic seed bacteriome in eight alpine grassland species growing at the Qinghai Tibetan Plateau. FEMS Microbiol Ecol 2021; 97:6246421. [PMID: 33885767 DOI: 10.1093/femsec/fiab060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
Seed borne microorganisms play an important role in plant biology. Concerns have recently been raised about loss of seed microbial diversity by seed treatments, crop domestication and plant breeding. Information on the seed microbiomes of native plants growing in natural ecosystems is beneficial as they provide the best settings to detect indigenous plant microbe interactions. Here, we characterized the seed bacterial community of 8 native alpine grassland plants. First, seed bacterial diversity was examined using Illumina DNA sequencing, then 28 cultivable bacteria were isolated and potential functions were explored. Across 8 plant species, 343 different bacterial genera were identified as seed endophytes, 31 of those were found in all plant species, indicating a high level of conservation. Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Chloroflexi were the top five dominant phyla. Plant species identity was a key determinant shaping the seed endophytic bacteriome. ACC deaminase activity, siderophores production and secretion of lytic enzymes were common functions shown by isolated bacteria. Our results demonstrate that highly diverse and beneficial bacterial populations are hosted by seeds of alpine grassland species to ensure the establishment of best bacterial symbionts for the next generation. This information is useful for crop improvement by reinstating beneficial seed microbial diversities for high-quality forage and crop seeds.
Collapse
Affiliation(s)
- Danni Liang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Jiayuguan West Roadd 768, Lanzhou, Gansu, 730020, China
| | - Jianxiu Guo
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Jiayuguan West Roadd 768, Lanzhou, Gansu, 730020, China
| | - Fujiang Hou
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Jiayuguan West Roadd 768, Lanzhou, Gansu, 730020, China
| | - Saman Bowatte
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Jiayuguan West Roadd 768, Lanzhou, Gansu, 730020, China.,AgResearch Limited, Grasslands Research Center, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| |
Collapse
|
42
|
Profiling, isolation and characterisation of beneficial microbes from the seed microbiomes of drought tolerant wheat. Sci Rep 2021; 11:11916. [PMID: 34099781 PMCID: PMC8184954 DOI: 10.1038/s41598-021-91351-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 05/18/2021] [Indexed: 11/09/2022] Open
Abstract
Climate change is predicted to increase the incidence and severity of drought conditions, posing a significant challenge for agriculture globally. Plant microbiomes have been demonstrated to aid crop species in the mitigation of drought stress. The study investigated the differences between the seed microbiomes of drought tolerant and drought susceptible wheat lines. Furthermore, it highlighted and quantified the degree of drought tolerance conferred by specific microbes isolated from drought tolerant wheat seed microbiomes. Metagenomic and culture-based methods were used to profile and characterise the seed microbiome composition of drought tolerant and drought susceptible wheat lines under rainfed and drought conditions. Isolates from certain genera were enriched by drought tolerant wheat lines when placed under drought stress. Wheat inoculated with isolates from these targeted genera, such as Curtobacterium flaccumfaciens (Cf D3-25) and Arthrobacter sp. (Ar sp. D4-14) demonstrated the ability to promote growth under drought conditions. This study indicates seed microbiomes from genetically distinct wheat lines enrich for beneficial bacteria in ways that are both line-specific and responsive to environmental stress. As such, seed from stress-phenotyped lines represent an invaluable resource for the identification of beneficial microbes with plant growth promoting activity that could improve commercial crop production.
Collapse
|
43
|
The Impact of Growth-Promoting Streptomycetes Isolated from Rhizosphere and Bulk Soil on Oilseed Rape (Brassica napus L.) Growth Parameters. SUSTAINABILITY 2021. [DOI: 10.3390/su13105704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Inoculation of Streptomyces to improve oilseed rape (Brassica napus L.) yields and minimise the use of chemical fertilisers is a promising sustainable strategy. In this study, we isolated 72 actinobacterial strains from rhizosphere of oilseed rape and maize and from bulk soil for screening and characterising their antimicrobial activity. Nine promising strains, identified as Streptomyces sp. by morphology, physiological characteristics, and 16S rRNA gene sequencing, were selected for their plant growth-promoting traits and in planta experiments. The actinobacterial strains were positive for IAA production, siderophore production, and HCN production. In planta experiments were conducted by soaking the oilseed rape seeds in the actinobacterial suspension, followed by plant growth under controlled conditions in a cultivate chamber (22–28 °C, 8 h dark/16 h light, constant humidity 80%). We recorded root and shoot length (cm) and seedling fresh weight (g). For most of the abovementioned parameters, a significant enhancement was observed with strain KmiRC20A118 treatment. The length of the root increased by 53.14%, the shoot length increased by 65.6%, and the weight of the fresh plant by 60% compared to the control. The integrated application of PGPS (Plant Growth Promoting Streptomyces) from the rhizosphere of oilseed rape is a promising strategy to improve the growth of oilseed rape.
Collapse
|
44
|
Chesneau G, Torres-Cortes G, Briand M, Darrasse A, Preveaux A, Marais C, Jacques MA, Shade A, Barret M. Temporal dynamics of bacterial communities during seed development and maturation. FEMS Microbiol Ecol 2021; 96:5910485. [PMID: 32966572 DOI: 10.1093/femsec/fiaa190] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 09/17/2020] [Indexed: 12/20/2022] Open
Abstract
Seed microbiota acts as a starting point for the assembly of the plant microbiota and contributes to successful plant establishment. To date, the order and timing of microbial taxa immigration during seed development and maturation remained unknown. We investigated the temporal dynamics of seed bacterial communities in bean and radish. A high phylogenetic turnover was observed for both plant species with few taxa associated with all seed developmental stages. Greater heterogeneity in communities structure within each stage was observed for radish. While, about one-third of radish seed bacterial taxa were detected in buds, flowers and fruits, very few taxa seem to be transmitted by the floral route in bean. In the latter species, bacterial populations belonging to the P. fluorescens species complex were found either in buds, flowers and fruits or in seeds. The relative phylogenetic proximity of these bacterial populations combined with their habitat specificity led us to explore the genetic determinants involved in successful seed transmission in bean. Comparative genomic analyses of representatives bacterial strains revealed dozens of coding sequences specifically associated with seed-transmitted strains. This study provided a first glimpse on processes involved in seed microbiota assembly, which could be used for designing plant-beneficial microbial consortia.
Collapse
Affiliation(s)
- Guillaume Chesneau
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Gloria Torres-Cortes
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Martial Briand
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Armelle Darrasse
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Anne Preveaux
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Coralie Marais
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Marie-Agnès Jacques
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Program in Ecology, Evolutionary Biology, and Behavior, The DOE Great Lakes Bioenergy Research Center, and The Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Matthieu Barret
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| |
Collapse
|
45
|
Faddetta T, Abbate L, Alibrandi P, Arancio W, Siino D, Strati F, De Filippo C, Fatta Del Bosco S, Carimi F, Puglia AM, Cardinale M, Gallo G, Mercati F. The endophytic microbiota of Citrus limon is transmitted from seed to shoot highlighting differences of bacterial and fungal community structures. Sci Rep 2021; 11:7078. [PMID: 33782436 PMCID: PMC8007603 DOI: 10.1038/s41598-021-86399-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 03/10/2021] [Indexed: 11/28/2022] Open
Abstract
Citrus limon (L.) Burm. F. is an important evergreen fruit crop whose rhizosphere and phyllosphere microbiota have been characterized, while seed microbiota is still unknown. Bacterial and fungal endophytes were isolated from C. limon surface-sterilized seeds. The isolated fungi—belonging to Aspergillus, Quambalaria and Bjerkandera genera—and bacteria—belonging to Staphylococcus genus—were characterized for indoleacetic acid production and phosphate solubilization. Next Generation Sequencing based approaches were then used to characterize the endophytic bacterial and fungal microbiota structures of surface-sterilized C. limon seeds and of shoots obtained under aseptic conditions from in vitro growing seedlings regenerated from surface-sterilized seeds. This analysis highlighted that Cutibacterium and Acinetobacter were the most abundant bacterial genera in both seeds and shoots, while Cladosporium and Debaryomyces were the most abundant fungal genera in seeds and shoots, respectively. The localization of bacterial endophytes in seed and shoot tissues was revealed by Fluorescence In Situ Hybridization coupled with Confocal Laser Scanning Microscopy revealing vascular bundle colonization. Thus, these results highlighted for the first time the structures of endophytic microbiota of C. limon seeds and the transmission to shoots, corroborating the idea of a vertical transmission of plant microbiota and suggesting its crucial role in seed germination and plant development.
Collapse
Affiliation(s)
- Teresa Faddetta
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Loredana Abbate
- Institute of Biosciences and Bioresources (IBBR), National Research Council, Palermo, Italy
| | - Pasquale Alibrandi
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Walter Arancio
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy.,Ri.MED Foundation, Palermo, Italy
| | - Davide Siino
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Francesco Strati
- Laboratory of Mucosal Immunology, Department of Experimental Oncology, European Institute of Oncology, Milano, Italy
| | - Carlotta De Filippo
- Institute of Agricultural Biology and Biotechnology, National Research Council, Pisa, Italy
| | - Sergio Fatta Del Bosco
- Institute of Biosciences and Bioresources (IBBR), National Research Council, Palermo, Italy
| | - Francesco Carimi
- Institute of Biosciences and Bioresources (IBBR), National Research Council, Palermo, Italy
| | - Anna Maria Puglia
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Massimiliano Cardinale
- Institute of Applied Microbiology, Justus-Liebig-University Giessen, Giessen, Germany.,Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
| | - Giuseppe Gallo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy.
| | - Francesco Mercati
- Institute of Biosciences and Bioresources (IBBR), National Research Council, Palermo, Italy
| |
Collapse
|
46
|
Gómez-Lama Cabanás C, Fernández-González AJ, Cardoni M, Valverde-Corredor A, López-Cepero J, Fernández-López M, Mercado-Blanco J. The Banana Root Endophytome: Differences between Mother Plants and Suckers and Evaluation of Selected Bacteria to Control Fusarium oxysporum f.sp. cubense. J Fungi (Basel) 2021; 7:jof7030194. [PMID: 33803181 PMCID: PMC8002102 DOI: 10.3390/jof7030194] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 12/13/2022] Open
Abstract
This study aimed to disentangle the structure, composition, and co-occurrence relationships of the banana (cv. Dwarf Cavendish) root endophytome comparing two phenological plant stages: mother plants and suckers. Moreover, a collection of culturable root endophytes (>1000) was also generated from Canary Islands. In vitro antagonism assays against Fusarium oxysporum f.sp. cubense (Foc) races STR4 and TR4 enabled the identification and characterization of potential biocontrol agents (BCA). Eventually, three of them were selected and evaluated against Fusarium wilt of banana (FWB) together with the well-known BCA Pseudomonas simiae PICF7 under controlled conditions. Culturable and non-culturable (high-throughput sequencing) approaches provided concordant information and showed low microbial diversity within the banana root endosphere. Pseudomonas appeared as the dominant genus and seemed to play an important role in the banana root endophytic microbiome according to co-occurrence networks. Fungal communities were dominated by the genera Ophioceras, Cyphellophora, Plecosphaerella, and Fusarium. Overall, significant differences were found between mother plants and suckers, suggesting that the phenological stage determines the recruitment and organization of the endophytic microbiome. While selected native banana endophytes showed clear antagonism against Foc strains, their biocontrol performance against FWB did not improve the outcome observed for a non-indigenous reference BCA (strain PICF7).
Collapse
Affiliation(s)
- Carmen Gómez-Lama Cabanás
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (CSIC), Campus ‘Alameda del Obispo’ s/n, Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain; (C.G.-L.C.); (M.C.); (A.V.-C.)
| | - Antonio J. Fernández-González
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Calle Profesor Albareda, 18008 Granada, Spain; (A.J.F.-G.); (M.F.-L.)
| | - Martina Cardoni
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (CSIC), Campus ‘Alameda del Obispo’ s/n, Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain; (C.G.-L.C.); (M.C.); (A.V.-C.)
| | - Antonio Valverde-Corredor
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (CSIC), Campus ‘Alameda del Obispo’ s/n, Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain; (C.G.-L.C.); (M.C.); (A.V.-C.)
| | - Javier López-Cepero
- Departamento Técnico de Coplaca S.C. Organización de Productores de Plátanos, Avd. de Anaga, 11-38001 Santa Cruz de Tenerife, Spain;
| | - Manuel Fernández-López
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Calle Profesor Albareda, 18008 Granada, Spain; (A.J.F.-G.); (M.F.-L.)
| | - Jesús Mercado-Blanco
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (CSIC), Campus ‘Alameda del Obispo’ s/n, Avd. Menéndez Pidal s/n, 14004 Córdoba, Spain; (C.G.-L.C.); (M.C.); (A.V.-C.)
- Correspondence: ; Tel.: +34-957-499261
| |
Collapse
|
47
|
Soldan R, Sanguankiattichai N, Bach-Pages M, Bervoets I, Huang WE, Preston GM. From macro to micro: a combined bioluminescence-fluorescence approach to monitor bacterial localization. Environ Microbiol 2021; 23:2070-2085. [PMID: 33103833 PMCID: PMC8614114 DOI: 10.1111/1462-2920.15296] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 01/13/2023]
Abstract
Bacterial bioluminescence is widely used to study the spatiotemporal dynamics of bacterial populations and gene expression in vivo at a population level but cannot easily be used to study bacterial activity at the level of individual cells. In this study, we describe the development of a new library of mini‐Tn7‐lux and lux::eyfp reporter constructs that provide a wide range of lux expression levels, and which combine the advantages of both bacterial bioluminescence and fluorescent proteins to bridge the gap between macro‐ and micro‐scale imaging techniques. We demonstrate that a dual bioluminescence‐fluorescence approach using the lux operon and eYFP can be used to monitor bacterial movement in plants both macro‐ and microscopically and demonstrate that Pseudomonas syringae pv phaseolicola can colonize the leaf vascular system and systemically infect leaves of common bean (Phaseolus vulgaris). We also show that bacterial bioluminescence can be used to study the impact of plant immune responses on bacterial multiplication, viability and spread within plant tissues. The constructs and approach described in this study can be used to study the spatiotemporal dynamics of bacterial colonization and to link population dynamics and cellular interactions in a wide range of biological contexts.
Collapse
Affiliation(s)
- Riccardo Soldan
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | | | - Indra Bervoets
- Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Wei E Huang
- Department of Engineering, University of Oxford, Oxford, UK
| | - Gail M Preston
- Department of Plant Sciences, University of Oxford, Oxford, UK
| |
Collapse
|
48
|
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.
Collapse
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
| |
Collapse
|
49
|
Kusstatscher P, Adam E, Wicaksono WA, Bernhart M, Olimi E, Müller H, Berg G. Microbiome-Assisted Breeding to Understand Cultivar-Dependent Assembly in Cucurbita pepo. FRONTIERS IN PLANT SCIENCE 2021; 12:642027. [PMID: 33897731 PMCID: PMC8063107 DOI: 10.3389/fpls.2021.642027] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/08/2021] [Indexed: 05/14/2023]
Abstract
Recently, it was shown that long-term plant breeding does not only shape plant characteristics but also impacts plant-associated microbiota substantially. This requires a microbiome-integrative breeding approach, which was not yet shown. Here we investigate this for the Styrian oil pumpkin (Cucurbita pepo L. subsp. pepo var. styriaca Greb.) by analyzing the microbiome of six genotypes (the complete pedigree of a three-way cross-hybrid, consisting of three inbred lines and one open pollinating cultivar) in the seed and rhizosphere as well as the progeny seeds. Using high-throughput amplicon sequencing targeting the 16S rRNA and the ITS1 genes, the bacterial and fungal microbiomes were accessed. Seeds were found to generally carry a significantly lower microbial diversity compared to the rhizosphere and soil as well as a different microbial composition, with an especially high fraction of Enterobacteriaceae (40-83%). Additionally, potential plant-beneficial bacterial taxa, including Bacillaceae, Burkholderiaceae, and Pseudomonadaceae, were found to be enriched in progeny seeds. Between genotypes, more substantial changes can be observed for seed microbiomes compared to the rhizosphere. Moreover, rhizosphere communities were assembled for the most part from soil. Interestingly, bacterial signatures are mainly linked from seed to seed, while fungal communities are shaped by the soil and rhizosphere. Our findings provide a deep look into the rhizosphere and seed microbiome assembly of pumpkin-associated communities and represent the first steps into microbiome-driven breeding for plant-beneficial microbes.
Collapse
Affiliation(s)
- Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- *Correspondence: Peter Kusstatscher,
| | - Eveline Adam
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Saatzucht Gleisdorf GmbH, Gleisdorf, Austria
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Expedito Olimi
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| |
Collapse
|
50
|
Matsumoto H, Fan X, Wang Y, Kusstatscher P, Duan J, Wu S, Chen S, Qiao K, Wang Y, Ma B, Zhu G, Hashidoko Y, Berg G, Cernava T, Wang M. Bacterial seed endophyte shapes disease resistance in rice. NATURE PLANTS 2021; 7:60-72. [PMID: 33398157 DOI: 10.1038/s41477-020-00826-5] [Citation(s) in RCA: 169] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 11/24/2020] [Indexed: 05/20/2023]
Abstract
Cereal crop production is severely affected by seed-borne bacterial diseases across the world. Locally occurring disease resistance in various crops remains elusive. Here, we have observed that rice plants of the same cultivar can be differentiated into disease-resistant and susceptible phenotypes under the same pathogen pressure. Following the identification of a seed-endophytic bacterium as the resistance-conferring agent, integration of high-throughput data, gene mutagenesis and molecular interaction assays facilitated the discovery of the underlying mode of action. Sphingomonas melonis that is accumulated and transmitted across generations in disease-resistant rice seeds confers resistance to disease-susceptible phenotypes by producing anthranilic acid. Without affecting cell growth, anthranilic acid interferes with the sigma factor RpoS of the seed-borne pathogen Burkholderia plantarii, probably leading to impairment of upstream cascades that are required for virulence factor biosynthesis. The overall findings highlight the hidden role of seed endophytes in the phytopathology paradigm of 'disease triangles', which encompass the plant, pathogens and environmental conditions. These insights are potentially exploitable for modern crop cultivation threatened by globally widespread bacterial diseases.
Collapse
Affiliation(s)
- Haruna Matsumoto
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Xiaoyan Fan
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Yue Wang
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Jie Duan
- Laboratory of Molecular and Ecological Chemistry, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Sanling Wu
- Analysis Center of Agrobiology and Environmental Sciences, Faculty of Agriculture, Life and Environment Sciences, Zhejiang University, Hangzhou, China
| | - Sunlu Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Kun Qiao
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Yiling Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Guonian Zhu
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Yasuyuki Hashidoko
- Laboratory of Molecular and Ecological Chemistry, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | - Mengcen Wang
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China.
| |
Collapse
|