1
|
Michl K, David C, Dumont B, Mårtensson LMD, Rasche F, Berg G, Cernava T. Determining the footprint of breeding in the seed microbiome of a perennial cereal. ENVIRONMENTAL MICROBIOME 2024; 19:40. [PMID: 38886863 PMCID: PMC11184768 DOI: 10.1186/s40793-024-00584-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/08/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND Seed endophytes have a significant impact on plant health and fitness. They can be inherited and passed on to the next plant generation. However, the impact of breeding on their composition in seeds is less understood. Here, we studied the indigenous seed microbiome of a recently domesticated perennial grain crop (Intermediate wheatgrass, Thinopyrum intermedium L.) that promises great potential for harnessing microorganisms to enhance crop performance by a multiphasic approach, including amplicon and strain libraries, as well as molecular and physiological assays. RESULTS Intermediate wheatgrass seeds harvested from four field sites in Europe over three consecutive years were dominated by Proteobacteria (88%), followed by Firmicutes (10%). Pantoea was the most abundant genus and Pantoea agglomerans was identified as the only core taxon present in all samples. While bacterial diversity and species richness were similar across all accessions, the relative abundance varied especially in terms of low abundant and rare taxa. Seeds from four different breeding cycles (TLI C3, C5, C704, C801) showed significant differences in bacterial community composition and abundance. We found a decrease in the relative abundance of the functional genes nirK and nifH as well as a drop in bacterial diversity and richness. This was associated with a loss of amplicon sequence variants (ASVs) in Actinobacteria, Alphaproteobacteria, and Bacilli, which could be partially compensated in offspring seeds, which have been cultivated at a new site. Interestingly, only a subset assigned to potentially beneficial bacteria, e.g. Pantoea, Kosakonia, and Pseudomonas, was transmitted to the next plant generation or shared with offspring seeds. CONCLUSION Overall, this study advances our understanding of the assembly and transmission of endophytic seed microorganisms in perennial intermediate wheatgrass and highlights the importance of considering the plant microbiome in future breeding programs.
Collapse
Affiliation(s)
- Kristina Michl
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
| | - Christophe David
- Department of Agroecosystems, Environment and Production, ISARA, 23 rue Jean Baldassini, Lyon Cedex 07, 69364, France
| | - Benjamin Dumont
- Plant Sciences Axis, Crop Science lab, ULiege - Gembloux Agro-Bio Tech, Gembloux, B- 5030, Belgium
| | | | - Frank Rasche
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, 70593, Stuttgart, Germany
- International Institute of Tropical Agriculture, P.O. Box 30772-00100, Nairobi, Kenya
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
- Leibnitz-Institute for Agricultural Engineering, 14469, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria.
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO171BJ, UK.
| |
Collapse
|
2
|
von Hoyningen-Huene AJE, Bang C, Rausch P, Rühlemann M, Fokt H, He J, Jensen N, Knop M, Petersen C, Schmittmann L, Zimmer T, Baines JF, Bosch TCG, Hentschel U, Reusch TBH, Roeder T, Franke A, Schulenburg H, Stukenbrock E, Schmitz RA. The archaeome in metaorganism research, with a focus on marine models and their bacteria-archaea interactions. Front Microbiol 2024; 15:1347422. [PMID: 38476944 PMCID: PMC10927989 DOI: 10.3389/fmicb.2024.1347422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/01/2024] [Indexed: 03/14/2024] Open
Abstract
Metaorganism research contributes substantially to our understanding of the interaction between microbes and their hosts, as well as their co-evolution. Most research is currently focused on the bacterial community, while archaea often remain at the sidelines of metaorganism-related research. Here, we describe the archaeome of a total of eleven classical and emerging multicellular model organisms across the phylogenetic tree of life. To determine the microbial community composition of each host, we utilized a combination of archaea and bacteria-specific 16S rRNA gene amplicons. Members of the two prokaryotic domains were described regarding their community composition, diversity, and richness in each multicellular host. Moreover, association with specific hosts and possible interaction partners between the bacterial and archaeal communities were determined for the marine models. Our data show that the archaeome in marine hosts predominantly consists of Nitrosopumilaceae and Nanoarchaeota, which represent keystone taxa among the porifera. The presence of an archaeome in the terrestrial hosts varies substantially. With respect to abundant archaeal taxa, they harbor a higher proportion of methanoarchaea over the aquatic environment. We find that the archaeal community is much less diverse than its bacterial counterpart. Archaeal amplicon sequence variants are usually host-specific, suggesting adaptation through co-evolution with the host. While bacterial richness was higher in the aquatic than the terrestrial hosts, a significant difference in diversity and richness between these groups could not be observed in the archaeal dataset. Our data show a large proportion of unclassifiable archaeal taxa, highlighting the need for improved cultivation efforts and expanded databases.
Collapse
Affiliation(s)
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Philipp Rausch
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Malte Rühlemann
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Hannover Medical School, Institute for Medical Microbiology and Hospital Epidemiology, Hannover, Germany
| | - Hanna Fokt
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jinru He
- Cell and Developmental Biology, Zoological Institute, Kiel University, Kiel, Germany
| | - Nadin Jensen
- Institute for General Microbiology, Kiel University, Kiel, Germany
| | - Mirjam Knop
- Department of Molecular Physiology, Zoology, Kiel University, Kiel, Germany
| | - Carola Petersen
- Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Lara Schmittmann
- Research Unit Ocean Dynamics, GEOMAR Helmholtz Institute for Ocean Research Kiel, Kiel, Germany
| | - Thorsten Zimmer
- Institute for General Microbiology, Kiel University, Kiel, Germany
- Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - John F. Baines
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Thomas C. G. Bosch
- Cell and Developmental Biology, Zoological Institute, Kiel University, Kiel, Germany
| | - Ute Hentschel
- Marine Evolutionary Ecology, GEOMAR Helmholtz Center for Ocean Research, Kiel, Germany
- Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Thorsten B. H. Reusch
- Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Thomas Roeder
- Department of Molecular Physiology, Zoology, Kiel University, Kiel, Germany
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Hinrich Schulenburg
- Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
- Antibiotic Resistance Group, Max-Planck Institute for Evolutionary Biology, Plön, Germany
| | - Eva Stukenbrock
- Max Planck Institute for Evolutionary Biology, Plön, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Ruth A. Schmitz
- Institute for General Microbiology, Kiel University, Kiel, Germany
| |
Collapse
|
3
|
Sharon O, Kagan-Trushina N, Sharon A. Wheat fungal endophyte communities are inseparable from the host and influence plant development. mBio 2024; 15:e0253323. [PMID: 38132833 PMCID: PMC10865843 DOI: 10.1128/mbio.02533-23] [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: 09/18/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
Plants harbor complex and highly diverse fungal endophyte communities (FECs), making it difficult to evaluate the functional role of individual taxa, subsets of the community, or the FEC as a whole. To reduce the complexity of this system, we aimed to produce fungi-null wheat (Triticum aestivum) plants. To this end, we treated seeds with heat and fungicides and generated plants from rescued embryos and callus tissue. A culture-based approach and reverse transcription PCR analysis were negative, indicating that all treatments produced plants apparently free of fungi. However, the analysis of DNA using digital droplet PCR and next-generation sequencing revealed that tissues from all treatments retained low levels but diversity-rich FECs. While the FECs varied in composition across treatments and tissues, they all included core taxa of the mycobiome. The reduced fungal biomass, along with the changes in FEC composition, negatively affected plant development, supporting a FEC contribution to proper plant development and fitness. Our discovery that a large part of the FEC cannot be separated from plants and can be transmitted through seeds and tissue culture calls for reevaluation of particular microbiome paradigms, such as core taxa concepts, transmission modes, and functional species.IMPORTANCEThe native microbiome in a given plant must be considered when evaluating the effect of a single taxon or synthetic community. The pre-existing microbiome can interact with artificially added microbial cargo, which affects the final outcome. Such issues can be at least partially solved by the use of endophyte-free plants, which provide a clean background that should be useful in determining the effect of a single taxon, taxa combinations, or the entire microbiome on plant performance. Previous reports regarded plants as endophyte-free or axenic by the lack of fungal growth on culture media or the generation of plants from tissue cultures. We showed here that while fungi could not be isolated from fungicide-treated or tissue culture-regenerated plants, nevertheless, all plants contained rich fungal endophyte communities; namely, it was impossible to create fungi-free wheat plants. Our results call for rethinking fundamental microbiome-related concepts, such as core taxa, transmission mode, and functional species.
Collapse
Affiliation(s)
- Or Sharon
- School of Plant Sciences and Food Security, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Institute for Cereal Crops Research, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Naomi Kagan-Trushina
- School of Plant Sciences and Food Security, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Amir Sharon
- School of Plant Sciences and Food Security, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Institute for Cereal Crops Research, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
4
|
Reid TE, Kavamura VN, Torres-Ballesteros A, Smith ME, Abadie M, Pawlett M, Clark IM, Harris JA, Mauchline TH. Agricultural intensification reduces selection of putative plant growth-promoting rhizobacteria in wheat. THE ISME JOURNAL 2024; 18:wrae131. [PMID: 38990206 PMCID: PMC11292143 DOI: 10.1093/ismejo/wrae131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/17/2024] [Accepted: 07/10/2024] [Indexed: 07/12/2024]
Abstract
The complex evolutionary history of wheat has shaped its associated root microbial community. However, consideration of impacts from agricultural intensification has been limited. This study investigated how endogenous (genome polyploidization) and exogenous (introduction of chemical fertilizers) factors have shaped beneficial rhizobacterial selection. We combined culture-independent and -dependent methods to analyze rhizobacterial community composition and its associated functions at the root-soil interface from a range of ancestral and modern wheat genotypes, grown with and without the addition of chemical fertilizer. In controlled pot experiments, fertilization and soil compartment (rhizosphere, rhizoplane) were the dominant factors shaping rhizobacterial community composition, whereas the expansion of the wheat genome from diploid to allopolyploid caused the next greatest variation. Rhizoplane-derived culturable bacterial collections tested for plant growth-promoting (PGP) traits revealed that fertilization reduced the abundance of putative plant growth-promoting rhizobacteria in allopolyploid wheats but not in wild wheat progenitors. Taxonomic classification of these isolates showed that these differences were largely driven by reduced selection of beneficial root bacteria representative of the Bacteroidota phylum in allopolyploid wheats. Furthermore, the complexity of supported beneficial bacterial populations in hexaploid wheats was greatly reduced in comparison to diploid wild wheats. We therefore propose that the selection of root-associated bacterial genera with PGP functions may be impaired by crop domestication in a fertilizer-dependent manner, a potentially crucial finding to direct future plant breeding programs to improve crop production systems in a changing environment.
Collapse
Affiliation(s)
- Tessa E Reid
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
- School of Water, Energy and Environment, Cranfield University, Cranfield, Bedfordshire MK43 0AL, United Kingdom
| | - Vanessa N Kavamura
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | | | - Monique E Smith
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - Maïder Abadie
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
- Present address: INRAE, UR1264 MycSA, CS2032, 33882 Villenave d’Ornon, France
| | - Mark Pawlett
- School of Water, Energy and Environment, Cranfield University, Cranfield, Bedfordshire MK43 0AL, United Kingdom
| | - Ian M Clark
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Jim A Harris
- School of Water, Energy and Environment, Cranfield University, Cranfield, Bedfordshire MK43 0AL, United Kingdom
| | - Tim H Mauchline
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| |
Collapse
|
5
|
Shen Y, Liu Y, Du Y, Wang X, Guan J, Jia X, Xu F, Song Z, Gao H, Zhang B, Guo P. Transfer of antibiotic resistance genes from soil to wheat: Role of host bacteria, impact on seed-derived bacteria, and affecting factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167279. [PMID: 37741386 DOI: 10.1016/j.scitotenv.2023.167279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/17/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023]
Abstract
The transfer of antibiotic resistance genes (ARGs) from soils to plants is poorly understood, especially the role of host bacteria in soils and its impact on seed-derived bacteria. Wheat (Triticum aestivum L.) was thus used to fill the gap by conducting pot experiments, with target ARGs and bacterial community analyzed. Results showed that the relative abundances of target ARGs gradually decreased during transfer of ARGs from the rhizosphere soil to root and shoot. Host bacteria in the rhizosphere soil were the primary source of ARGs in wheat. The 38, 21, and 19 potential host bacterial genera of target ARGs and intI1 in the rhizosphere soil, root, and shoot were identified, respectively, and they mainly belonged to phylum Proteobacteria. The abundance of ARGs carried by pathogenic Corynebacterium was reduced in sequence. During transfer of ARGs from the rhizosphere soil to root and shoot, some seed-derived bacteria and pathogenic Acinetobacter obtained ARGs through horizontal gene transfer and became potential host bacteria. Furthermore, total organic carbon, available nitrogen of the rhizosphere soil, water use efficiency, vapor pressure deficit, and superoxide dismutase of plants were identified as the key factors affecting potential host bacteria transfer in soils to wheat. This work provides important insights into transfer of ARGs and deepens our understanding of potential health risks of ARGs from soils to plants.
Collapse
Affiliation(s)
- Yanping Shen
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Yibo Liu
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Yutong Du
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Xu Wang
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Jiunian Guan
- School of Environment, Northeast Normal University, Changchun 130117, PR China
| | - Xiaohui Jia
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Fukai Xu
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Ziwei Song
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Hongjie Gao
- Chinese Research Academy of Environmental Science, Beijing 100012, PR China.
| | - Baiyu Zhang
- Department of Civil Engineering, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3X5, Canada.
| | - Ping Guo
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China.
| |
Collapse
|
6
|
Zeng Q, Zhao Y, Shen W, Han D, Yang M. Seed-to-Seed: Plant Core Vertically Transmitted Microbiota. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19255-19264. [PMID: 38044571 DOI: 10.1021/acs.jafc.3c07092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The plant core microbiota transmitted by seeds have been demonstrated to exist in seeds and adult plants of several crops for multiple generations. They are closely related to plants and are relatively conserved throughout evolution, domestication, and breeding. These microbiota play a vital role in the early stages of plant growth. However, information about their colonization routes, transmission pathways, and final fate remains fragmentary. This review delves into the concept of these microbiota, their colonization sources, transmission pathways, and how they change throughout plant evolution, domestication, and breeding, as well as their effects on plants, based on relevant literature. Finally, the significant potential of incorporating the practical application of seed-transmitted microbiota into plant microbial breeding is emphasized.
Collapse
Affiliation(s)
- Quan Zeng
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yang Zhao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei Shen
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dejun Han
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingming Yang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| |
Collapse
|
7
|
Sun Z, Adeleke BS, Shi Y, Li C. The seed microbiomes of staple food crops. Microb Biotechnol 2023; 16:2236-2249. [PMID: 37815330 PMCID: PMC10686132 DOI: 10.1111/1751-7915.14352] [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: 05/23/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/11/2023] Open
Abstract
The scientific community increasingly recognized that seed microbiomes are important for plant growth and nutrition. The versatile roles and modulating properties that microbiomes hold in the context of seeds seem to be an inherited approach to avert adverse conditions. These discoveries attracted extensive interest, especially in staple food crops (SFCs) where grain was consumed as food. Along with the rapid expansion of population and industrialization that posed a severe challenge to the yield of SFCs, microbiologists and botanists began to explore and engineer seed microbiomes, for safer and more fruitful grain production. To utilize seed microbiomes, we present an overall review of the most updated scientific literature on three representative SFCs (wheat, rice and maize) using the 5W1H (Which, Where, What, Why, When and How) method that provides a comprehensive understanding of the issue. These include which factors determine the composition of seed microbiomes? Where do seed microbiomes come from? What are these seed microbes? Why do these microbes choose seeds as their destination and when do microbes settle down and become seed communists? In addition, how do seed microbiomes work and can be manipulated effectively? Therefore, answering the aforementioned questions regarding SFCs seed microbiomes remain fundamental in bridging endophytic research gaps and harnessing their ecological services.
Collapse
Affiliation(s)
- Zhongke Sun
- School of Biological EngineeringHenan University of TechnologyZhengzhouChina
- Food Laboratory of ZhongyuanLuoheChina
| | - Bartholomew Saanu Adeleke
- School of Biological EngineeringHenan University of TechnologyZhengzhouChina
- Department of Biological Sciences, School of ScienceOlusegun Agagu University of Science and TechnologyOkitipupaNigeria
| | - Yini Shi
- School of Biological EngineeringHenan University of TechnologyZhengzhouChina
| | - Chengwei Li
- School of Biological EngineeringHenan University of TechnologyZhengzhouChina
| |
Collapse
|
8
|
Sun X, Sharon O, Sharon A. Distinct Features Based on Partitioning of the Endophytic Fungi of Cereals and Other Grasses. Microbiol Spectr 2023; 11:e0061123. [PMID: 37166321 PMCID: PMC10269846 DOI: 10.1128/spectrum.00611-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/18/2023] [Indexed: 05/12/2023] Open
Abstract
Endophytic fungi form a significant part of the plant mycobiome. Defining core members is crucial to understanding the assembly mechanism of fungal endophytic communities (FECs) and identifying functionally important community members. We conducted a meta-analysis of FECs in stems of wheat and five wild cereal species and generated a landscape of the fungal endophytic assemblages in this group of plants. The analysis revealed that several Ascomycota members and basidiomycetous yeasts formed an important compartment of the FECs in these plants. We observed a weak spatial autocorrelation at the regional scale and high intrahost variations in the FECs, suggesting a space-related heterogeneity. Accordingly, we propose that the heterogeneity among subcommunities should be a criterion to define the core endophytic members. Analysis of the subcommunities and meta-communities showed that the core and noncore members had distinct roles in various assembly processes, such as stochasticity, universal dynamics, and network characteristics, within each host. The distinct features identified between the community partitions of endophytes aid in understanding the principles that govern the assembly and function of natural communities. These findings can assist in designing synthetic microbiomes. IMPORTANCE This study proposes a novel method for diagnosing core microbiotas based on prevalence of community members in a meta-community, which could be determined and supported statistically. Using this approach, the study found stratification in community assembly processes within fungal endophyte communities (FECs) in the stems of wheat and cereal-related wild species. The core and noncore partitions of the FECs exhibited certain degrees of determinism from different aspects. Further analysis revealed abundant and consistent interactions between rare taxa, which might contribute to the determinism process in noncore partitions. Despite minor differences in FEC compositions, wheat FECs showed distinct patterns in community assembly processes compared to wild species, suggesting the effects of domestication on FECs. Overall, our study provided a new approach for identifying core microbiota and provides insights into the community assembly processes within FECs in wheat and related wild species.
Collapse
Affiliation(s)
- Xiang Sun
- School of Life Sciences, Hebei University, Baoding, Hebei, China
| | - Or Sharon
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Amir Sharon
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
9
|
PhyloPlus: a Universal Tool for Phylogenetic Interrogation of Metagenomic Communities. mBio 2023; 14:e0345522. [PMID: 36645293 PMCID: PMC9973285 DOI: 10.1128/mbio.03455-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Phylogeny is a powerful tool that can be incorporated into quantitative descriptions of community diversity, yet its use has been limited largely due to the difficulty in constructing phylogenies which incorporate the wide genomic diversity of microbial communities. Here, we describe the development of a web portal, PhyloPlus, which enables users to generate customized phylogenies that may be applied to any bacterial or archaeal communities. We demonstrate the power of phylogeny by comparing metrics that employ phylogeny with those that do not when applied to data sets from two metagenomic studies (fermented food, n = 58; human microbiome, n = 60). This example shows how inclusion of all bacterial species identified by taxonomic classifiers (Kraken2 and Kaiju) made the phylogeny perfectly congruent to the corresponding classification outputs. Our phylogeny-based approach also enabled the construction of more constrained null models which (i) shed light into community structure and (ii) minimize potential inflation of type I errors. Construction of such null models allowed for the observation of under-dispersion in 44 (75.86%) food samples, with the metacommunity defined as bacteria that were found in different food matrices. We also observed that closely related species with high abundance and uneven distribution across different sites could potentially exaggerate the dissimilarity between phylogenetically similar communities if they were measured using traditional species-based metrics (Padj. = 0.003), whereas this effect was mitigated by incorporating phylogeny (Padj. = 1). In summary, our tool can provide additional insights into microbial communities of interest and facilitate the use of phylogeny-based approaches in metagenomic analyses. IMPORTANCE There has been an explosion of interest in how microbial diversity affects human health, food safety, and environmental functions among many other processes. Accurately measuring the diversity and structure of those communities is central to understanding their effects. Here, we describe the development of a freely available online tool, PhyloPlus, which allows users to generate custom phylogenies that may be applied to any data set, thereby removing a major obstacle to the application of phylogeny to metagenomic data analysis. We demonstrate that the genetic relatedness of the organisms within those communities is a critical feature of their overall diversity, and that using a phylogeny which captures and quantifies this diversity allows for much more accurate descriptions while preventing misleading conclusions based on estimates that ignore evolutionary relationships.
Collapse
|
10
|
Abstract
The genus Bacillus has been widely applied in contemporary agriculture as an environmentally-friendly biological agent. However, the real effect of commercial Bacillus-based fertilizers and pesticides varies immensely in the field. To harness Bacillus for efficient wheat production, we reviewed the diversity, functionality, and applicability of wheat-associated native Bacillus for the first time. Our main findings are: (i) Bacillus spp. inhabit the rhizosphere, root, stem, leaf, and kernel of wheat; (ii) B. subtilis and B. velezensis are the most widely endophytic species that can be isolated from both below and aboveground tissues; (iii) major functions of these representative strains are promotion of plant growth and alleviation of both abiotic and biotic stresses in wheat; (iv) stability and effectiveness are 2 major challenges during field application; (v) a STVAE pipeline that includes 5 processes, namely, Screen, Test, Validation, Application, and Evaluation, has been proposed for the capture and refinement of wheat-associated Bacillus spp. In particular, this review comprehensively addresses possible solutions, concerns, and criteria during the development of native Bacillus-based inoculants for sustainable wheat production.
Collapse
|
11
|
Aswini K, Suman A, Sharma P, Singh PK, Gond S, Pathak D. Seed endophytic bacterial profiling from wheat varieties of contrasting heat sensitivity. FRONTIERS IN PLANT SCIENCE 2023; 14:1101818. [PMID: 37089648 PMCID: PMC10117849 DOI: 10.3389/fpls.2023.1101818] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/10/2023] [Indexed: 05/03/2023]
Abstract
Wheat yield can be limited by many biotic and abiotic factors. Heat stress at the grain filling stage is a factor that reduces wheat production tremendously. The potential role of endophytic microorganisms in mitigating plant stress through various biomolecules like enzymes and growth hormones and also by improving plant nutrition has led to a more in-depth exploration of the plant microbiome for such functions. Hence, we devised this study to investigate the abundance and diversity of wheat seed endophytic bacteria (WSEB) from heatS (heat susceptible, GW322) and heatT (heat tolerant, HD3298 and HD3271) varieties by culturable and unculturable approaches. The results evidenced that the culturable diversity was higher in the heatS variety than in the heatT variety and Bacillus was found to be dominant among the 10 different bacterial genera identified. Though the WSEB population was higher in the heatS variety, a greater number of isolates from the heatT variety showed tolerance to higher temperatures (up to 55°C) along with PGP activities such as indole acetic acid (IAA) production and nutrient acquisition. Additionally, the metagenomic analysis of seed microbiota unveiled higher bacterial diversity, with a predominance of the phyla Proteobacteria covering >50% of OTUs, followed by Firmicutes and Actinobacteria. There were considerable variations in the abundance and diversity between heat sensitivity contrasting varieties, where notably more thermophilic bacterial OTUs were observed in the heatT samples, which could be attributed to conferring tolerance against heat stress. Furthermore, exploring the functional characteristics of culturable and unculturable microbiomes would provide more comprehensive information on improving plant growth and productivity for sustainable agriculture.
Collapse
Affiliation(s)
- Krishnan Aswini
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Archna Suman
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Archna Suman,
| | - Pushpendra Sharma
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pradeep Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shrikant Gond
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Devashish Pathak
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| |
Collapse
|
12
|
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
|
13
|
Characteristics of rhizosphere and endogenous bacterial community of Ulleung-sanmaneul, an endemic plant in Korea: application for alleviating salt stress. Sci Rep 2022; 12:21124. [PMID: 36476722 PMCID: PMC9729608 DOI: 10.1038/s41598-022-25731-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
Microbes influence plant growth and fitness. However, the structure and function of microbiomes associated with rare and endemic plants remain underexplored. To investigate the bacterial community structure of Ulleung-sanmaneul (U-SMN), an endemic plant in Korea, samples were collected from natural and cultivated habitats, and their 16S rDNA was sequenced. The root bacterial community structure differed from those of bulk soil and rhizosphere in both habitats. Endogenous bacteria in cultivated plants were less diverse than wild plants, but Luteibacter rhizovicinus, Pseudomonas fulva, and Sphingomonas pruni were shared. Co-inoculation of Pseudoxanthomonas sp. JBCE485 and Variovorax paradoxus JBCE486 promoted growth and induced salt stress resistance in Arabidopsis and chive. Changes in growth promotion and phenotypes of plants by co-inoculation were mediated by increased auxin production. Each strain colonized the roots without niche competition. The results indicated that host selectivity was influential than environmental factors in formulating endophytic bacterial composition, and domestication simplified the bacterial community diversity. Our results will contribute to the growth and maintenance of endemic U-SMN plants.
Collapse
|
14
|
Zapién-Campos R, Bansept F, Sieber M, Traulsen A. On the effect of inheritance of microbes in commensal microbiomes. BMC Ecol Evol 2022; 22:75. [PMID: 35710335 PMCID: PMC9204957 DOI: 10.1186/s12862-022-02029-2] [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: 09/24/2021] [Accepted: 06/02/2022] [Indexed: 11/10/2022] Open
Abstract
Background Our current view of nature depicts a world where macroorganisms dwell in a landscape full of microbes. Some of these microbes not only transit but establish themselves in or on hosts. Although hosts might be occupied by microbes for most of their lives, a microbe-free stage during their prenatal development seems to be the rule for many hosts. The questions of who the first colonizers of a newborn host are and to what extent these are obtained from the parents follow naturally. Results We have developed a mathematical model to study the effect of the transfer of microbes from parents to offspring. Even without selection, we observe that microbial inheritance is particularly effective in modifying the microbiome of hosts with a short lifespan or limited colonization from the environment, for example by favouring the acquisition of rare microbes. Conclusion By modelling the inheritance of commensal microbes to newborns, our results suggest that, in an eco-evolutionary context, the impact of microbial inheritance is of particular importance for some specific life histories. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02029-2.
Collapse
|
15
|
Gutierrez A, Grillo MA. Effects of Domestication on Plant-Microbiome Interactions. PLANT & CELL PHYSIOLOGY 2022; 63:1654-1666. [PMID: 35876043 DOI: 10.1093/pcp/pcac108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 07/15/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Through the process of domestication, selection is targeted on a limited number of plant traits that are typically associated with yield. As an unintended consequence, domesticated plants often perform poorly compared to their wild progenitors for a multitude of traits that were not under selection during domestication, including abiotic and biotic stress tolerance. Over the past decade, advances in sequencing technology have allowed for the rigorous characterization of host-associated microbial communities, termed the microbiome. It is now clear that nearly every conceivable plant interaction with the environment is mediated by interactions with the microbiome. For this reason, plant-microbiome interactions are an area of great promise for plant breeding and crop improvement. Here, we review the literature to assess the potential impact that domestication has had on plant-microbiome interactions and the current understanding of the genetic basis of microbiome variation to inform plant breeding efforts. Overall, we find limited evidence that domestication impacts the diversity of microbiomes, but domestication is often associated with shifts in the abundance and composition of microbial communities, including taxa of known functional significance. Moreover, genome-wide association studies and mutant analysis have not revealed a consistent set of core candidate genes or genetic pathways that confer variation in microbiomes across systems. However, such studies do implicate a consistent role for plant immunity, root traits, root and leaf exudates and cell wall integrity as key traits that control microbiome colonization and assembly. Therefore, selection on these key traits may pose the most immediate promise for enhancing plant-microbiome interactions through breeding.
Collapse
Affiliation(s)
- Andres Gutierrez
- Department of Biology, Loyola University Chicago, 1032 W. Sheridan Rd, Chicago, IL 60660, USA
| | - Michael A Grillo
- Department of Biology, Loyola University Chicago, 1032 W. Sheridan Rd, Chicago, IL 60660, USA
| |
Collapse
|
16
|
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
|
17
|
Özkurt E, Fritscher J, Soranzo N, Ng DYK, Davey RP, Bahram M, Hildebrand F. LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis. MICROBIOME 2022; 10:176. [PMID: 36258257 PMCID: PMC9580208 DOI: 10.1186/s40168-022-01365-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 09/01/2022] [Indexed: 05/02/2023]
Abstract
BACKGROUND Amplicon sequencing is an established and cost-efficient method for profiling microbiomes. However, many available tools to process this data require both bioinformatics skills and high computational power to process big datasets. Furthermore, there are only few tools that allow for long read amplicon data analysis. To bridge this gap, we developed the LotuS2 (less OTU scripts 2) pipeline, enabling user-friendly, resource friendly, and versatile analysis of raw amplicon sequences. RESULTS In LotuS2, six different sequence clustering algorithms as well as extensive pre- and post-processing options allow for flexible data analysis by both experts, where parameters can be fully adjusted, and novices, where defaults are provided for different scenarios. We benchmarked three independent gut and soil datasets, where LotuS2 was on average 29 times faster compared to other pipelines, yet could better reproduce the alpha- and beta-diversity of technical replicate samples. Further benchmarking a mock community with known taxon composition showed that, compared to the other pipelines, LotuS2 recovered a higher fraction of correctly identified taxa and a higher fraction of reads assigned to true taxa (48% and 57% at species; 83% and 98% at genus level, respectively). At ASV/OTU level, precision and F-score were highest for LotuS2, as was the fraction of correctly reported 16S sequences. CONCLUSION LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. AVAILABILITY LotuS2 is available from GitHub, conda, or via a Galaxy web interface, documented at http://lotus2.earlham.ac.uk/ . Video Abstract.
Collapse
Affiliation(s)
- Ezgi Özkurt
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK
| | - Joachim Fritscher
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK
| | - Nicola Soranzo
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK
| | - Duncan Y K Ng
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Robert P Davey
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51, Uppsala, Sweden
- Institute of Ecology and Earth Sciences, University of Tartu, Lai St, 40, Tartu, Estonia
| | - Falk Hildebrand
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK.
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK.
| |
Collapse
|
18
|
Jacquiod S, Raynaud T, Pimet E, Ducourtieux C, Casieri L, Wipf D, Blouin M. Wheat Rhizosphere Microbiota Respond to Changes in Plant Genotype, Chemical Inputs, and Plant Phenotypic Plasticity. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.903008] [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
Modern wheat varieties that were selected since the Green Revolution are generally grown with synthetic chemical inputs, and ancient varieties released before1960 without. Thus, when changes occur in rhizosphere microbiota structure, it is not possible to distinguish if they are due to (i) changes in wheat genotypes by breeding, (ii) modifications of the environment via synthetic chemical inputs, or (iii) phenotypic plasticity, the interaction between wheat genotype and the environment. Using a crossed factorial design in the field, we evaluated the effects of either modern or ancient wheat varieties grown with or without chemical inputs (a N fertilizer, a fungicide, and an herbicide) on “microbiome as a phenotype.” We analyzed the rhizosphere microbiota by bacterial and fungal amplicon sequencing, coupled with microscope observations of mycorrhizal associations. We found that plant genotype and phenotypic plasticity had the most influence on rhizosphere microbiota, whereas inputs had only marginal effects. Phenotypic plasticity was particularly important in explaining diversity variations in bacteria and fungi but had no impact on the mycorrhizal association. Our results show an interest in considering the interaction between wheat genotype and the environment in breeding programs, by focusing on genes involved in the phenotypic plasticity of plant-microbe interactions.
Collapse
|
19
|
Seed-Derived Microbial Community of Wild Cicer Seedlings: Composition and Augmentation to Domesticated Cicer. Microbiol Spectr 2022; 10:e0278521. [PMID: 35638782 PMCID: PMC9241877 DOI: 10.1128/spectrum.02785-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Seed-borne bacteria are a unique group of microorganisms capable of maintaining stable populations within plant tissues and seeds. These bacteria may benefit their host from germination to maturation and are of great interest for basic and applied plant-microbe interaction studies. Furthermore, many such beneficial bacteria present in wild plant species are missing in their respective congeneric domesticated forms. The objectives of this study were to explore the bacterial communities within the seeds of wild Cicer species and to select beneficial bacteria which could be used to improve production of domesticated chickpea (C. arietinum). We analyzed the composition of seed-borne bacteria of chickpea (Cicer spp.), comparing wild and domesticated species from different geographic locations. Subsequently, we isolated the dominant and prevalent seed-borne bacteria from wild Cicer judaicum and assessed their ability to colonize and affect the growth of domesticated chickpea and other legume crops. The composition and structure of seed-borne bacteria, determined by amplicon sequencing of the 16S rRNA gene, differed between wild and domesticated chickpea and varied among geographic locations. The genus Burkholderia dominated samples from domesticated chickpea at all examined sites, while Bacillus or Sphingomonas dominated cultures isolated from wild C. judaicum, dependent on geographic location. A particular Bacillus strain, Bacillus sp. CJ, representing the most prevalent bacterium in wild C. judaicum, was further isolated. Bacillus sp. CJ, applied by seed coating, successfully inhabited domesticated chickpea plants and improved plant growth parameters. These results demonstrate the potential for reconstructing the microbiota of crop plants using the wild microbiota reservoir. IMPORTANCE Chickpea (garbanzo bean, hummus, Cicer arietinum) representing the third legume crop produced globally. As is the case for many other domesticated crops, the adaptation and resistance of chickpea to biotic and abiotic stresses is inferior compared to that of their wild progenitors and relatives. Re-establishing desirable characteristics from wild to domesticated species may be achieved by reconstructing beneficial microbiota. In this study, we examined the seed-associated microbiota of both wild and domesticated chickpea and applied isolated beneficial bacteria originating from wild Cicer judaicum to domesticated chickpea by seed coating. This isolate, Bacillus sp. CJ, was successfully established in the crop and enhanced its growth, demonstrating effective and efficient manipulation of the chickpea microbiota as a potential model for future application in other crop plants.
Collapse
|
20
|
The Role of Soil Microbial Diversity in the Conservation of Native Seed Bacterial Microbiomes. Microorganisms 2022; 10:microorganisms10040750. [PMID: 35456799 PMCID: PMC9028870 DOI: 10.3390/microorganisms10040750] [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: 02/24/2022] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 11/29/2022] Open
Abstract
Research into understanding the structure, composition and vertical transmission of crop seed microbiomes has intensified, although there is much less research into the seed microbiomes of crop wild relatives. Our previous study showed that the standard seed storage procedures (e.g., seed drying and storage temperature) can influence the seed microbiome of domesticated Glycine max. In this study, we characterized the seed microbiota of Glycine clandestina, a perennial wild relative of soybean (G. max (L.) Merr.) to expand our understanding about the effect of other storage procedures such as the periodic regeneration of seed stocks to bulk up seed numbers and secure viability on the seed microbiome of said seed. The G. clandestina microbiota was analysed from Generation 1 (G1) and Generation 2 (G2) seed and from mature plant organs grown in two different soil treatments T (treatment [native soil + potting mix]) and C (control [potting mix only]). Our dataset showed that soil microbiota had a strong influence on next generation seed microbiota, with an increased contribution of root microbiota by 90% and seed transmissibility by 36.3% in G2 (T) seed. Interestingly, the G2 seed microbiota primarily consisted of an initially low abundance of taxa present in G1 seed. Overall, our results indicate that seed regeneration can affect the seed microbiome composition and using native soil from the location of the source plant can enhance the conservation of the native seed microbiota.
Collapse
|
21
|
Analysis of seed-associated bacteria and fungi on staple crops using the cultivation and metagenomic approaches. Folia Microbiol (Praha) 2022; 67:351-361. [PMID: 35220558 PMCID: PMC9072454 DOI: 10.1007/s12223-022-00958-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/09/2022] [Indexed: 11/04/2022]
Abstract
AbstractOne of the key factors affecting seed quality is microbial communities residing on and in the seeds. In this study, microbial populations of seeds of conventionally and organically produced wheat, barley, and maize were analyzed using two different approaches: the cultivation method and metagenomics. For cultivation, three basic media were used: DG18 (for fungi), and nutrient agar or tryptic soy agar supplemented with cycloheximide or nystatin (for bacteria). Metagenomic sequencing was performed using the Illumina MiSeq platform. A total of 452 bacterial isolates comprising 36 genera and 5 phyla and 90 fungal isolates comprising 10 genera and 3 phyla were obtained from the seed surfaces. Among bacteria, representatives from the genera Bacillus, Pantoea, Paenibacillus, and Curtobacterium predominated, and among fungi, Aspergillus predominated. A total of 142 fungal OTUs and 201 bacterial OTUs were obtained from all the samples. Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria comprised most of the bacterial OTUs, and Ascomycota comprised most of the fungal OTUs. Only 3 fungal OTUs (representatives of Curvibasidium, Venturia, and Dermateaceae) were exclusively present only within seeds and not on the seed surfaces. Barley seeds had the highest microbial load and richness, whereas corn had the lowest. Wheat and barley shared a higher number of OTUs than either of them did with corn with higher overlap between conventionally grown cereals than between organically grown cereals. Some OTUs were farming specific. This study demonstrates that the microbiome of cereal seeds is greatly dependent on the species of the host and is less affected by agricultural practices.
Collapse
|
22
|
Gholizadeh S, Mohammadi SA, Salekdeh GH. Changes in root microbiome during wheat evolution. BMC Microbiol 2022; 22:64. [PMID: 35219318 PMCID: PMC8881823 DOI: 10.1186/s12866-022-02467-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 02/08/2022] [Indexed: 12/20/2022] Open
Abstract
Abstract
Background
Although coevolutionary signatures of host-microbe interactions are considered to engineer the healthy microbiome of humans, little is known about the changes in root-microbiome during plant evolution. To understand how the composition of the wheat and its ancestral species microbiome have changed over the evolutionary processes, we performed a 16S rRNA metagenomic analysis on rhizobacterial communities associated with a phylogenetic framework of four Triticum species T. urartu, T. turgidum, T. durum, and T. aestivum along with their ancestral species Aegilops speltoides, and Ae. tauschii during vegetative and reproductive stages.
Results
In this study, we illustrated that the genome contents of wild species Aegilops speltoides and Ae. tauschii can be significant factors determining the composition of root-associated bacterial communities in domesticated bread wheat. Although it was found that domestication and modern breeding practices might have had a significant impact on microbiome-plant interactions especially at the reproductive stage, we observed an extensive and selective control by wheat genotypes on associated rhizobacterial communities at the same time. Our data also showed a strong genotypic variation within species of T. aestivum and Ae. tauschii, suggesting potential breeding targets for plants surveyed.
Conclusions
This study performed with different genotypes of Triticum and Aegilops species is the first study showing that the genome contents of Ae. speltoides and Ae. tauschii along with domestication-related changes can be significant factors determining the composition of root-associated bacterial communities in bread wheat. It is also indirect evidence that shows a very extensive range of host traits and genes are probably involved in host-microbe interactions. Therefore, understanding the wheat root-associated microbiome needs to take into consideration of its polygenetic mosaic nature.
Collapse
|
23
|
Gruet C, Muller D, Moënne-Loccoz Y. Significance of the Diversification of Wheat Species for the Assembly and Functioning of the Root-Associated Microbiome. Front Microbiol 2022; 12:782135. [PMID: 35058901 PMCID: PMC8764353 DOI: 10.3389/fmicb.2021.782135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/30/2021] [Indexed: 12/15/2022] Open
Abstract
Wheat, one of the major crops in the world, has had a complex history that includes genomic hybridizations between Triticum and Aegilops species and several domestication events, which resulted in various wild and domesticated species (especially Triticum aestivum and Triticum durum), many of them still existing today. The large body of information available on wheat-microbe interactions, however, was mostly obtained without considering the importance of wheat evolutionary history and its consequences for wheat microbial ecology. This review addresses our current understanding of the microbiome of wheat root and rhizosphere in light of the information available on pre- and post-domestication wheat history, including differences between wild and domesticated wheats, ancient and modern types of cultivars as well as individual cultivars within a given wheat species. This analysis highlighted two major trends. First, most data deal with the taxonomic diversity rather than the microbial functioning of root-associated wheat microbiota, with so far a bias toward bacteria and mycorrhizal fungi that will progressively attenuate thanks to the inclusion of markers encompassing other micro-eukaryotes and archaea. Second, the comparison of wheat genotypes has mostly focused on the comparison of T. aestivum cultivars, sometimes with little consideration for their particular genetic and physiological traits. It is expected that the development of current sequencing technologies will enable to revisit the diversity of the wheat microbiome. This will provide a renewed opportunity to better understand the significance of wheat evolutionary history, and also to obtain the baseline information needed to develop microbiome-based breeding strategies for sustainable wheat farming.
Collapse
Affiliation(s)
| | | | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), VetAgro Sup, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| |
Collapse
|
24
|
Nunes I, Hansen V, Bak F, Bonnichsen L, Su J, Hao X, Raymond NS, Nicolaisen MH, Jensen LS, Nybroe O. OUP accepted manuscript. FEMS Microbiol Ecol 2022; 98:6548193. [PMID: 35285907 PMCID: PMC8951222 DOI: 10.1093/femsec/fiac028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/22/2022] [Accepted: 03/10/2022] [Indexed: 11/21/2022] Open
Abstract
During germination, the seed releases nutrient-rich exudates into the spermosphere, thereby fostering competition between resident microorganisms. However, insight into the composition and temporal dynamics of seed-associated bacterial communities under field conditions is currently lacking. This field study determined the temporal changes from 11 to 31 days after sowing in the composition of seed-associated bacterial communities of winter wheat as affected by long-term soil fertilization history, and by introduction of the plant growth-promoting microbial inoculants Penicillium bilaiae and Bacillus simplex. The temporal dynamics were the most important factor affecting the composition of the seed-associated communities. An increase in the relative abundance of genes involved in organic nitrogen metabolism (ureC and gdhA), and in ammonium oxidation (amoA), suggested increased mineralization of plant-derived nitrogen compounds over time. Dynamics of the phosphorus cycling genes ppt, ppx and cphy indicated inorganic phosphorus and polyphosphate cycling, as well as phytate hydrolysis by the seed-associated bacteria early after germination. Later, an increase in genes for utilization of organic phosphorus sources (phoD, phoX and phnK) indicated phosphorus limitation. The results indicate that community temporal dynamics are partly driven by changed availability of major nutrients, and reveal no functional consequences of the added inoculants during seed germination.
Collapse
Affiliation(s)
| | | | | | - Lise Bonnichsen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Jianqiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xiuli Hao
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University; Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Nelly Sophie Raymond
- Plant and Soil Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensevej 40, 1871 Frederiksberg C, Denmark
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Mette Haubjerg Nicolaisen
- Corresponding author: Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, Univeristy of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark. Tel: +45 35332649; E-mail:
| | - Lars Stoumann Jensen
- Plant and Soil Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensevej 40, 1871 Frederiksberg C, Denmark
| | - Ole Nybroe
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| |
Collapse
|
25
|
González-Benítez N, Martín-Rodríguez I, Cuesta I, Arrayás M, White JF, Molina MC. Endophytic Microbes Are Tools to Increase Tolerance in Jasione Plants Against Arsenic Stress. Front Microbiol 2021; 12:664271. [PMID: 34690941 PMCID: PMC8527096 DOI: 10.3389/fmicb.2021.664271] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/08/2021] [Indexed: 01/04/2023] Open
Abstract
Seed microbiota is becoming an emergent area of research. Host plant microbial diversity is increasingly well described, yet relatively little is known about the stressors driving plant endomicrobiota at the metaorganism level. The present work examines the role of horizontal and vertical transmission of bacterial microbiota in response to abiotic stress generated by arsenic. Horizontal transmission is achieved by bioaugmentation with the endophyte Rhodococcus rhodochrous, while vertical transmission comes via maternal inheritance from seeds. To achieve this goal, all experiments were conducted with two Jasione species. J. montana is tolerant to arsenic (As), whereas J. sessiliflora, being phylogenetically close to J. montana, was not previously described as As tolerant. The Jasione core bacterial endophytes are composed of genera Pseudomonas, Ralstonia, Undibacterium, Cutibacterium, and Kocuria and family Comamanadaceae across different environmental conditions. All these operational taxonomic units (OTUs) coexisted from seeds to the development of the seedling, independently of As stress, or bioaugmentation treatment and Jasione species. R. rhodochrous colonized efficiently both species, driving the endomicrobiota structure of Jasione with a stronger effect than As stress. Despite the fact that most of the OTUs identified inside Jasione seeds and seedlings belonged to rare microbiota, they represent a large bacterial reservoir offering important physiological and ecological traits to the host. Jasione traits co-regulated with R. rhodochrous, and the associated microbiota improved the host response to As stress. NGS-Illumina tools provided further knowledge about the ecological and functional roles of plant endophytes.
Collapse
Affiliation(s)
- Natalia González-Benítez
- Department of Biology, Geology, Physics, and Inorganic Chemistry, Universidad Rey Juan Carlos, Madrid, Spain
| | - Irene Martín-Rodríguez
- Department of Biology, Geology, Physics, and Inorganic Chemistry, Universidad Rey Juan Carlos, Madrid, Spain
| | - Isabel Cuesta
- Unidad de Bioinformática, Instituto de Salud Carlos III, Madrid, Spain
| | - Manuel Arrayás
- Área de Electromagnetismo, Universidad Rey Juan Carlos, Madrid, Spain
| | - James Francis White
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, United States
| | - María Carmen Molina
- Department of Biology, Geology, Physics, and Inorganic Chemistry, Universidad Rey Juan Carlos, Madrid, Spain.,Department of Plant Biology, Rutgers University, New Brunswick, NJ, United States
| |
Collapse
|
26
|
Kim H, Lee YH. Spatiotemporal Assembly of Bacterial and Fungal Communities of Seed-Seedling-Adult in Rice. Front Microbiol 2021; 12:708475. [PMID: 34421867 PMCID: PMC8375405 DOI: 10.3389/fmicb.2021.708475] [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: 05/12/2021] [Accepted: 07/19/2021] [Indexed: 01/04/2023] Open
Abstract
Seeds harbor not only genetic information about plants but also microbial communities affecting plants’ vigor. Knowledge on the movement and formation of seed microbial communities during plant development remains insufficient. Here, we address this knowledge gap by investigating endophytic bacterial and fungal communities of seeds, seedlings, and adult rice plants. We found that seed coats act as microbial niches for seed bacterial and fungal communities. The presence or absence of the seed coat affected taxonomic composition and diversity of bacterial and fungal communities associated with seeds and seedlings. Ordination analysis showed that niche differentiation between above- and belowground compartments leads to compositional differences in endophytic bacterial and fungal communities originating from seeds. Longitudinal tracking of the composition of microbial communities from field-grown rice revealed that bacterial and fungal communities originating from seeds persist in the leaf, stem, and root endospheres throughout the life cycle. Our study provides ecological insights into the assembly of the initial endophytic microbial communities of plants from seeds.
Collapse
Affiliation(s)
- Hyun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea.,Center for Fungal Genetic Resources, Seoul National University, Seoul, South Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea.,Plant Immunity Research Center, Seoul National University, Seoul, South Korea
| |
Collapse
|
27
|
Soldan R, Fusi M, Cardinale M, Daffonchio D, Preston GM. The effect of plant domestication on host control of the microbiota. Commun Biol 2021; 4:936. [PMID: 34354230 PMCID: PMC8342519 DOI: 10.1038/s42003-021-02467-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 07/16/2021] [Indexed: 02/07/2023] Open
Abstract
Macroorganisms are colonized by microbial communities that exert important biological and ecological functions, the composition of which is subject to host control and has therefore been described as "an ecosystem on a leash". However, domesticated organisms such as crop plants are subject to both artificial selection and natural selection exerted by the agricultural ecosystem. Here, we propose a framework for understanding how host control of the microbiota is influenced by domestication, in which a double leash acts from domesticator to host and host to microbes. We discuss how this framework applies to a plant compartment that has demonstrated remarkable phenotypic changes during domestication: the seed.
Collapse
Affiliation(s)
- Riccardo Soldan
- University of Oxford, Department of Plant Sciences, Oxford, UK.
| | - Marco Fusi
- Edinburgh Napier University, School of Applied Sciences, Edinburgh, UK
| | - Massimiliano Cardinale
- University of Salento, Department of Biological and Environmental Sciences and Technologies, Lecce, Italy
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal, Saudi Arabia
| | - Gail M Preston
- University of Oxford, Department of Plant Sciences, Oxford, UK.
| |
Collapse
|
28
|
Abstract
The seed microbial community constitutes an initial inoculum for plant microbiota assembly. Still, the persistence of seed microbiota when seeds encounter soil during plant emergence and early growth is barely documented. We characterized the encounter event of seed and soil microbiota and how it structured seedling bacterial and fungal communities by using amplicon sequencing. We performed eight contrasting encounter events to identify drivers influencing seedling microbiota assembly. To do so, four contrasting seed lots of two Brassica napus genotypes were sown in two soils whose microbial diversity levels were manipulated by serial dilution and recolonization. Seedling root and stem microbiota were influenced by soil but not by initial seed microbiota composition or by plant genotype. A strong selection on the seed and soil communities occurred during microbiota assembly, with only 8% to 32% of soil taxa and 0.8% to 1.4% of seed-borne taxa colonizing seedlings. The recruitment of seedling microbiota came mainly from soil (35% to 72% of diversity) and not from seeds (0.3% to 15%). Soil microbiota transmission success was higher for the bacterial community than for the fungal community. Interestingly, seedling microbiota was primarily composed of initially rare taxa (from seed, soil, or unknown origin) and intermediate-abundance soil taxa. IMPORTANCE Seed microbiota can have a crucial role for crop installation by modulating dormancy, germination, seedling development, and recruitment of plant symbionts. Little knowledge is available on the fraction of the plant microbiota that is acquired through seeds. We characterize the encounter between seed and soil communities and how they colonize the seedling together. Transmission success and seedling community assemblage can be influenced by the variation of initial microbial pools, i.e., plant genotype and cropping year for seeds and diversity level for soils. Despite a supposed resident advantage of the seed microbiota, we show that transmission success is in favor of the soil microbiota. Our results also suggest that successful plant-microbiome engineering based on native seed or soil microbiota must include rare taxa.
Collapse
|
29
|
Bacterial Endophytes of Spring Wheat Grains and the Potential to Acquire Fe, Cu, and Zn under Their Low Soil Bioavailability. BIOLOGY 2021; 10:biology10050409. [PMID: 34063099 PMCID: PMC8148187 DOI: 10.3390/biology10050409] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/27/2021] [Accepted: 05/01/2021] [Indexed: 11/30/2022]
Abstract
Simple Summary Unmasking the overall endophytic bacteria communities from wheat grains may help to identify and describe the microbial colonization of bread and emmer varieties, their link to the bioactive compounds produced, and their possible role in mineral nutrition. The possibility of using microorganisms to improve the microelemental composition of grain is an important food security concern, as approximately one-third of the human population experiences latent starvation caused by Fe (anemia), Zn, or Cu deficiency. Four wheat varieties from T. aestivum L. and T. turgidum subsp. dicoccum were grown in field conditions with low bioavailability of microelements in the soil. Varietal differences in the yield, yield characteristics, and the grain micronutrient concentrations were compared with the endophytic bacteria isolated from the grains. Twelve different bacterial isolates were obtained that represented the genera Staphylococcus, Pantoea, Sphingobium, Bacillus, Kosakonia, and Micrococcus. All studied strains were able to synthesize indole-related compounds (IRCs) with phytohormonal activity. IRCs produced by the bacterial genera Pantoea spp. and Bacillus spp. isolated from high-yielding Oksamyt myronivs’kyi and Holikovs’ka grains may be considered as one of the determinants of the yield of wheat and its nutritional characteristics. Abstract Wheat grains are usually low in essential micronutrients. In resolving the problem of grain micronutritional quality, microbe-based technologies, including bacterial endophytes, seem to be promising. Thus, we aimed to (1) isolate and identify grain endophytic bacteria from selected spring wheat varieties (bread Oksamyt myronivs’kyi, Struna myronivs’ka, Dubravka, and emmer Holikovs’ka), which were all grown in field conditions with low bioavailability of microelements, and (2) evaluate the relationship between endophytes’ abilities to synthesize auxins and the concentration of Fe, Zn, and Cu in grains. The calculated biological accumulation factor (BAF) allowed for comparing the varietal ability to uptake and transport micronutrients to the grains. For the first time, bacterial endophytes were isolated from grains of emmer wheat T. turgidum subsp. dicoccum. Generally, the 12 different isolates identified in the four varieties belonged to the genera Staphylococcus, Pantoea, Sphingobium, Bacillus, Kosakonia, and Micrococcus (NCBI accession numbers: MT302194—MT302204, MT312840). All the studied strains were able to synthesize the indole-related compounds (IRCs; max: 16.57 µg∙mL−1) detected using the Salkowski reagent. The IRCs produced by the bacterial genera Pantoea spp. and Bacillus spp. isolated from high-yielding Oksamyt myronivs’kyi and Holikovs’ka grains may be considered as one of the determinants of the yield of wheat and its nutritional characteristics.
Collapse
|
30
|
Soluch R, Hülter NF, Romero Picazo D, Özkurt E, Stukenbrock EH, Dagan T. Colonization dynamics of Pantoea agglomerans in the wheat root habitat. Environ Microbiol 2021; 23:2260-2273. [PMID: 33587819 DOI: 10.1111/1462-2920.15430] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 02/09/2021] [Indexed: 01/27/2023]
Abstract
Plants are colonized by microbial communities that have diverse implications for plant development and health. The establishment of a stable plant-bacteria interaction depends on a continuous coexistence over generations. Transmission via the seed is considered as the main route for vertical inheritance of plant-associated bacteria. Nonetheless, the ecological principles that govern the plant colonization by seed endophytes remain understudied. Here we quantify the contribution of arrival time and colonization history to bacterial colonization of the wheat root. Establishing a common seed endophyte, Pantoea agglomerans, and wheat as a model system enabled us to document bacterial colonization of the plant roots during the early stages of germination. Using our system, we estimate the carrying capacity of the wheat roots as 108 cells g-1 , which is robust among individual plants and over time. Competitions in planta reveal a significant advantage of early incoming colonizers over late-incoming colonizers. Priming for the wheat environment had little effect on the colonizer success. Our experiments thus provide empirical data on the root colonization dynamics of a seed endophyte. The persistence of seed endophyte bacteria with the plant population over generations may contribute to the stable transmission that is one route for the evolution of a stable host-associated lifestyle.
Collapse
Affiliation(s)
- Ryszard Soluch
- Institute of General Microbiology, Christian-Albrechts University of Kiel, Am Botanischen Garten 11, Kiel, 24118, Germany
| | - Nils F Hülter
- Institute of General Microbiology, Christian-Albrechts University of Kiel, Am Botanischen Garten 11, Kiel, 24118, Germany
| | - Devani Romero Picazo
- Institute of General Microbiology, Christian-Albrechts University of Kiel, Am Botanischen Garten 11, Kiel, 24118, Germany
| | - Ezgi Özkurt
- Environmental Genomics, Christian-Albrechts University of Kiel, Am Botanischen Garten 1-9, Kiel, 24118, Germany.,Environmental Genomics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, Plön, 24306, Germany
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University of Kiel, Am Botanischen Garten 1-9, Kiel, 24118, Germany.,Environmental Genomics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, Plön, 24306, Germany
| | - Tal Dagan
- Institute of General Microbiology, Christian-Albrechts University of Kiel, Am Botanischen Garten 11, Kiel, 24118, Germany
| |
Collapse
|