151
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New frontiers in agriculture productivity: Optimised microbial inoculants and in situ microbiome engineering. Biotechnol Adv 2019; 37:107371. [PMID: 30890361 DOI: 10.1016/j.biotechadv.2019.03.010] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/20/2019] [Accepted: 03/11/2019] [Indexed: 01/07/2023]
Abstract
Increasing agricultural productivity is critical to feed the ever-growing human population. Being linked intimately to plant health, growth and productivity, harnessing the plant microbiome is considered a potentially viable approach for the next green revolution, in an environmentally sustainable way. In recent years, our understanding of drivers, roles, mechanisms, along with knowledge to manipulate the plant microbiome, have significantly advanced. Yet, translating this knowledge to expand farm productivity and sustainability requires the development of solutions for a number of technological and logistic challenges. In this article, we propose new and emerging strategies to improve the survival and activity of microbial inoculants, including using selected indigenous microbes and optimising microbial delivery methods, as well as modern gene editing tools to engineer microbial inoculants. In addition, we identify multiple biochemical and molecular mechanisms and/approaches which can be exploited for microbiome engineering in situ to optimise plant-microbiome interactions for improved farm yields. These novel biotechnological approaches can provide effective tools to attract and maintain activities of crop beneficial microbiota that increase crop performance in terms of nutrient acquisition, and resistance to biotic and abiotic stresses, resulting in an increased agricultural productivity and sustainability.
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152
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Adaptations and evolution of a heritable leaf nodule symbiosis between Dioscorea sansibarensis and Orrella dioscoreae. ISME JOURNAL 2019; 13:1831-1844. [PMID: 30877285 DOI: 10.1038/s41396-019-0398-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/05/2019] [Accepted: 03/05/2019] [Indexed: 12/31/2022]
Abstract
Various plant species establish intimate symbioses with bacteria within their aerial organs. The bacteria are contained within nodules or glands often present in distinctive patterns on the leaves in what is commonly referred to as leaf nodule symbiosis. We describe here a highly specific symbiosis between a wild yam species from Madagascar, Dioscorea sansibarensis and bacteria of the species Orrella dioscoreae. Using whole-genome sequencing of plastids and bacteria from wild-collected samples, we show phylogenetic patterns consistent with a dominant vertical mode of transmission of the symbionts. Unique so far among leaf nodule symbioses, the bacteria can be cultured and are amenable to comparative transcriptomics, revealing a potential role in complementing the host's arsenal of secondary metabolites. We propose a recent establishment of a vertical mode of transmission in this symbiosis which, together with a large effective population size explains the cultivability and apparent lack of genome reductive evolution in O. dioscoreae. We leverage these unique features to reveal pathways and functions under positive selection in these specialized endophytes, highlighting the candidate mechanisms enabling a permanent association in the phyllosphere.
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153
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Jongsma MA, Thoen MPM, Poleij LM, Wiegers GL, Goedhart PW, Dicke M, Noldus LPJJ, Kruisselbrink JW. An Integrated System for the Automated Recording and Analysis of Insect Behavior in T-maze Arrays. FRONTIERS IN PLANT SCIENCE 2019; 10:20. [PMID: 30761167 PMCID: PMC6361829 DOI: 10.3389/fpls.2019.00020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 01/08/2019] [Indexed: 05/11/2023]
Abstract
Host-plant resistance to insects like thrips and aphids is a complex trait that is difficult to phenotype quickly and reliably. Here, we introduce novel hardware and software to facilitate insect choice assays and automate the acquisition and analysis of movement tracks. The hardware consists of an array of individual T-mazes allowing simultaneous release of up to 90 insect individuals from their individual cage below each T-maze with choice of two leaf disks under a video camera. Insect movement tracks are acquired with computer vision software (EthoVision) and analyzed with EthoAnalysis, a novel software package that allows for automated reporting of highly detailed behavior parameters and statistical analysis. To validate the benefits of the system we contrasted two Arabidopsis accessions that were previously analyzed for differential resistance to western flower thrips. Results of two trials with 40 T-mazes are reported and we show how we arrived at optimized settings for the different filters and statistics. The statistics are reported in terms of frequency, duration, distance and speed of behavior events, both as sum totals and event averages, and both for the total trial period and in time bins of 1 h. Also included are higher level analyses with subcategories like short-medium-long events and slow-medium-fast events. The time bins showed how some behavior elements are more descriptive of differences between the genotypes during the first hours, whereas others are constant or become more relevant at the end of an 8 h recording. The three overarching behavior categories, i.e., choice, movement, and halting, were automatically corrected for the percentage of time thrips were detected and 24 out of 38 statistics of behavior parameters differed by a factor 2-6 between the accessions. The analysis resulted in much larger contrasts in behavior traits than reported previously. Compared to leaf damage assays on whole plants or detached leaves that take a week or more to complete, results were obtained in 8 h, with more detail, fewer individuals and higher significance. The potential value of the new integrated system, named EntoLab, for discovery of genetic traits in plants and insects by high throughput screening of large populations is discussed.
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Affiliation(s)
- Maarten A. Jongsma
- Wageningen Plant Research, Wageningen University and Research, Wageningen, Netherlands
| | - Manus P. M. Thoen
- Wageningen Plant Research, Wageningen University and Research, Wageningen, Netherlands
- Laboratory of Entomology, Wageningen University and Research, Wageningen, Netherlands
| | - Leo M. Poleij
- Wageningen Plant Research, Wageningen University and Research, Wageningen, Netherlands
| | - Gerrie L. Wiegers
- Wageningen Plant Research, Wageningen University and Research, Wageningen, Netherlands
| | - Paul W. Goedhart
- Wageningen Plant Research, Wageningen University and Research, Wageningen, Netherlands
| | - Marcel Dicke
- Laboratory of Entomology, Wageningen University and Research, Wageningen, Netherlands
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154
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Susi H, Filloux D, Frilander MJ, Roumagnac P, Laine AL. Diverse and variable virus communities in wild plant populations revealed by metagenomic tools. PeerJ 2019; 7:e6140. [PMID: 30648011 PMCID: PMC6330959 DOI: 10.7717/peerj.6140] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/20/2018] [Indexed: 12/21/2022] Open
Abstract
Wild plant populations may harbour a myriad of unknown viruses. As the majority of research efforts have targeted economically important plant species, the diversity and prevalence of viruses in the wild has remained largely unknown. However, the recent shift towards metagenomics-based sequencing methodologies, especially those targeting small RNAs, is finally enabling virus discovery from wild hosts. Understanding this diversity of potentially pathogenic microbes in the wild can offer insights into the components of natural biodiversity that promotes long-term coexistence between hosts and parasites in nature, and help predict when and where risks of disease emergence are highest. Here, we used small RNA deep sequencing to identify viruses in Plantago lanceolata populations, and to understand the variation in their prevalence and distribution across the Åland Islands, South-West Finland. By subsequent design of PCR primers, we screened the five most common viruses from two sets of P. lanceolata plants: 164 plants collected from 12 populations irrespective of symptoms, and 90 plants collected from five populations showing conspicuous viral symptoms. In addition to the previously reported species Plantago lanceolata latent virus (PlLV), we found four potentially novel virus species belonging to Caulimovirus, Betapartitivirus, Enamovirus, and Closterovirus genera. Our results show that virus prevalence and diversity varied among the sampled host populations. In six of the virus infected populations only a single virus species was detected, while five of the populations supported between two to five of the studied virus species. In 20% of the infected plants, viruses occurred as coinfections. When the relationship between conspicuous viral symptoms and virus infection was investigated, we found that plants showing symptoms were usually infected (84%), but virus infections were also detected from asymptomatic plants (44%). Jointly, these results reveal a diverse virus community with newly developed tools and protocols that offer exciting opportunities for future studies on the eco-evolutionary dynamics of viruses infecting plants in the wild.
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Affiliation(s)
- Hanna Susi
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland
| | - Denis Filloux
- CIRAD, BGPI, Montpellier, France.,BGPI, INRA, CIRAD, SupAgro, University Montpellier, Montpellier, France
| | - Mikko J Frilander
- Institute of Biotechnology, Genome Biology Program, University of Helsinki, Finland
| | - Philippe Roumagnac
- CIRAD, BGPI, Montpellier, France.,BGPI, INRA, CIRAD, SupAgro, University Montpellier, Montpellier, France
| | - Anna-Liisa Laine
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland
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155
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Bergelson J, Mittelstrass J, Horton MW. Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome. Sci Rep 2019; 9:24. [PMID: 30631088 PMCID: PMC6328596 DOI: 10.1038/s41598-018-37208-z] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 11/30/2018] [Indexed: 12/14/2022] Open
Abstract
Roots provide plants mineral nutrients and stability in soil; while doing so, they come into contact with diverse soil microbes that affect plant health and productivity. Despite their ecological and agricultural relevance, the factors that shape the root microbiome remain poorly understood. We grew a worldwide panel of replicated Arabidopsis thaliana accessions outdoors and over winter to characterize their root-microbial communities. Although studies of the root microbiome tend to focus on bacteria, we found evidence that fungi have a strong influence on the structure of the root microbiome. Moreover, host effects appear to have a stronger influence on plant-fungal communities than plant-bacterial communities. Mapping the host genes that affect microbiome traits identified a priori candidate genes with roles in plant immunity; the root microbiome also appears to be strongly affected by genes that impact root and root hair development. Our results suggest that future analyses of the root microbiome should focus on multiple kingdoms, and that the root microbiome is shaped not only by genes involved in defense, but also by genes involved in plant form and physiology.
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Affiliation(s)
- Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Jana Mittelstrass
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Matthew W Horton
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland.
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156
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Rootstocks Shape the Rhizobiome: Rhizosphere and Endosphere Bacterial Communities in the Grafted Tomato System. Appl Environ Microbiol 2019; 85:AEM.01765-18. [PMID: 30413478 DOI: 10.1128/aem.01765-18] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/23/2018] [Indexed: 12/21/2022] Open
Abstract
Root-associated microbes are critical to plant health and performance, although understanding of the factors that structure these microbial communities and the theory to predict microbial assemblages are still limited. Here, we use a grafted tomato system to study the effects of rootstock genotypes and grafting in endosphere and rhizosphere microbiomes that were evaluated by sequencing 16S rRNA. We compared the microbiomes of nongrafted tomato cultivar BHN589, self-grafted BHN589, and BHN589 grafted to Maxifort or RST-04-106 hybrid rootstocks. Operational taxonomic unit (OTU)-based bacterial diversity was greater in Maxifort compared to the nongrafted control, whereas bacterial diversity in the controls (self-grafted and nongrafted) and the other rootstock (RST-04-106) was similar. Grafting itself did not affect bacterial diversity; diversity in the self-graft was similar to that of the nongraft. Bacterial diversity was higher in the rhizosphere than in the endosphere for all treatments. However, despite the lower overall diversity, there was a greater number of differentially abundant OTUs (DAOTUs) in the endosphere, with the greatest number of DAOTUs associated with Maxifort. In a permutational multivariate analysis of variance (PERMANOVA), there was evidence for an effect of rootstock genotype on bacterial communities. The endosphere-rhizosphere compartment and study site explained a high percentage of the differences among bacterial communities. Further analyses identified OTUs responsive to rootstock genotypes in both the endosphere and rhizosphere. Our findings highlight the effects of rootstocks on bacterial diversity and composition. The influence of rootstock and plant compartment on microbial communities indicates opportunities for the development of designer communities and microbiome-based breeding to improve future crop production.IMPORTANCE Understanding factors that control microbial communities is essential for designing and supporting microbiome-based agriculture. In this study, we used a grafted tomato system to study the effect of rootstock genotypes and grafting on bacterial communities colonizing the endosphere and rhizosphere. To compare the bacterial communities in control treatments (nongrafted and self-grafted plants) with the hybrid rootstocks used by farmers, we evaluated the effect of rootstocks on overall bacterial diversity and composition. These findings indicate the potential for using plant genotype to indirectly select bacterial taxa. In addition, we identify taxa responsive to each rootstock treatment, which may represent candidate taxa useful for biocontrol and in biofertilizers.
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157
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Cheng D, Tian Z, Feng L, Xu L, Wang H. Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range. PeerJ 2019; 6:e6162. [PMID: 30643678 PMCID: PMC6327885 DOI: 10.7717/peerj.6162] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 11/25/2018] [Indexed: 11/20/2022] Open
Abstract
Increasing evidence has confirmed the importance of plant-associated bacteria for plant growth and productivity, and thus it is hypothesized that interactions between bacteria and alien plants might play an important role in plant invasions. However, the diversity of the bacterial communities associated with invasive plants is poorly understood. We therefore investigated the diversity of rhizospheric and endophytic bacteria associated with the invasive annual plant Senecio vulgaris L. (Asteraceae) based on 16S rRNA gene data obtained from 57 samples of four Senecio vulgaris populations in a subtropical mountainous area in central China. Significant differences in diversity were observed between plant compartments. Specifically, the rhizosphere harbored many more bacterial operational taxonomic units and showed higher alpha diversity than the leaf and root endospheres. The relative abundance profiles of the bacterial community composition differed substantially between the compartments and populations, especially at the phylum and family levels. However, the top five phyla (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Acidobacteria) accounted for more than 90% of all the bacterial communities. Moreover, similar endophytic communities with a shared core set of bacteria were observed from different Senecio vulgaris populations. Heavy-metal-resistant, phosphate-solubilizing bacteria (Brevundimonas diminuta), nitrogen-fixing bacteria (Rhizobium leguminosarum), and cold-resistant bacteria (Exiguobacterium sibiricum) were present in the endosphere at relatively high abundance. This study, which reveals the structure of bacterial communities and their putative function in invasive Senecio vulgaris plants, is the first step in investigating the role of plant-bacteria interactions in the invasion of this species in China.
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Affiliation(s)
- Dandan Cheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, China
| | - Zhongsai Tian
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| | - Liang Feng
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| | - Lin Xu
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, China
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158
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Wille L, Messmer MM, Studer B, Hohmann P. Insights to plant-microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes. PLANT, CELL & ENVIRONMENT 2019; 42:20-40. [PMID: 29645277 DOI: 10.1111/pce.13214] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 05/19/2023]
Abstract
Root and foot diseases severely impede grain legume cultivation worldwide. Breeding lines with resistance against individual pathogens exist, but these resistances are often overcome by the interaction of multiple pathogens in field situations. Novel tools allow to decipher plant-microbiome interactions in unprecedented detail and provide insights into resistance mechanisms that consider both simultaneous attacks of various pathogens and the interplay with beneficial microbes. Although it has become clear that plant-associated microbes play a key role in plant health, a systematic picture of how and to what extent plants can shape their own detrimental or beneficial microbiome remains to be drawn. There is increasing evidence for the existence of genetic variation in the regulation of plant-microbe interactions that can be exploited by plant breeders. We propose to consider the entire plant holobiont in resistance breeding strategies in order to unravel hidden parts of complex defence mechanisms. This review summarizes (a) the current knowledge of resistance against soil-borne pathogens in grain legumes, (b) evidence for genetic variation for rhizosphere-related traits, (c) the role of root exudation in microbe-mediated disease resistance and elaborates (d) how these traits can be incorporated in resistance breeding programmes.
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Affiliation(s)
- Lukas Wille
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), 5070, Frick, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, 8092, Zurich, Switzerland
| | - Monika M Messmer
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), 5070, Frick, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, 8092, Zurich, Switzerland
| | - Pierre Hohmann
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), 5070, Frick, Switzerland
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159
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Beilsmith K, Thoen MPM, Brachi B, Gloss AD, Khan MH, Bergelson J. Genome-wide association studies on the phyllosphere microbiome: Embracing complexity in host-microbe interactions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:164-181. [PMID: 30466152 DOI: 10.1111/tpj.14170] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 11/08/2018] [Accepted: 11/16/2018] [Indexed: 05/18/2023]
Abstract
Environmental sequencing shows that plants harbor complex communities of microbes that vary across environments. However, many approaches for mapping plant genetic variation to microbe-related traits were developed in the relatively simple context of binary host-microbe interactions under controlled conditions. Recent advances in sequencing and statistics make genome-wide association studies (GWAS) an increasingly promising approach for identifying the plant genetic variation associated with microbes in a community context. This review discusses early efforts on GWAS of the plant phyllosphere microbiome and the outlook for future studies based on human microbiome GWAS. A workflow for GWAS of the phyllosphere microbiome is then presented, with particular attention to how perspectives on the mechanisms, evolution and environmental dependence of plant-microbe interactions will influence the choice of traits to be mapped.
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Affiliation(s)
- Kathleen Beilsmith
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th St, Chicago, IL, 60637, USA
| | - Manus P M Thoen
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th St, Chicago, IL, 60637, USA
| | - Benjamin Brachi
- BIOGECO, INRA, University of Bordeaux, 33610, Cestas, France
| | - Andrew D Gloss
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th St, Chicago, IL, 60637, USA
| | - Mohammad H Khan
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th St, Chicago, IL, 60637, USA
| | - Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th St, Chicago, IL, 60637, USA
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160
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Su J, Zhang F, Chong X, Song A, Guan Z, Fang W, Chen F. Genome-wide association study identifies favorable SNP alleles and candidate genes for waterlogging tolerance in chrysanthemums. HORTICULTURE RESEARCH 2019; 6:21. [PMID: 30729011 PMCID: PMC6355785 DOI: 10.1038/s41438-018-0101-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 08/06/2018] [Accepted: 10/09/2018] [Indexed: 05/05/2023]
Abstract
Chrysanthemums are sensitive to waterlogging stress, and the development of screening methods for tolerant germplasms or genes and the breeding of tolerant new varieties are of great importance in chrysanthemum breeding. To understand the genetic basis of waterlogging tolerance (WT) in chrysanthemums, we performed a genome-wide association study (GWAS) using 92,811 single nucleotide polymorphisms (SNPs) in a panel of 88 chrysanthemum accessions, including 64 spray cut and 24 disbud chrysanthemums. The results showed that the average MFVW (membership function value of waterlogging) of the disbud type (0.65) was significantly higher than that of the spray type (0.55) at P < 0.05, and the MFVW of the Asian accessions (0.65) was significantly higher than that of the European accessions (0.48) at P < 0.01. The GWAS performed using the general linear model (GLM) and mixed linear model (MLM) identified 137 and 14 SNP loci related to WT, respectively, and 11 associations were commonly predicted. By calculating the phenotypic effect values for 11 common SNP loci, six highly favorable SNP alleles that explained 12.85-21.85% of the phenotypic variations were identified. Furthermore, the dosage-pyramiding effects of the favorable alleles and the significant linear correlations between the numbers of highly favorable alleles and phenotypic values were identified (r 2 = 0.45; P < 0.01). A major SNP locus (Marker6619-75) was converted into a derived cleaved amplified polymorphic sequence (dCAPS) marker that cosegregated with WT with an average efficiency of 78.9%. Finally, four putative candidate genes in the WT were identified via quantitative real-time PCR (qRT-PCR). The results presented in this study provide insights for further research on WT mechanisms and the application of molecular marker-assisted selection (MAS) in chrysanthemum WT breeding programs.
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Affiliation(s)
- Jiangshuo Su
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Fei Zhang
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Xinran Chong
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Aiping Song
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
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161
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Zaidem ML, Groen SC, Purugganan MD. Evolutionary and ecological functional genomics, from lab to the wild. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:40-55. [PMID: 30444573 DOI: 10.1111/tpj.14167] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/10/2018] [Accepted: 11/13/2018] [Indexed: 05/12/2023]
Abstract
Plant phenotypes are the result of both genetic and environmental forces that act to modulate trait expression. Over the last few years, numerous approaches in functional genomics and systems biology have led to a greater understanding of plant phenotypic variation and plant responses to the environment. These approaches, and the questions that they can address, have been loosely termed evolutionary and ecological functional genomics (EEFG), and have been providing key insights on how plants adapt and evolve. In particular, by bringing these studies from the laboratory to the field, EEFG studies allow us to gain greater knowledge of how plants function in their natural contexts.
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Affiliation(s)
- Maricris L Zaidem
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
| | - Simon C Groen
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
| | - Michael D Purugganan
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY, 10003, USA
- Center for Genomics and Systems Biology, NYU Abu Dhabi Research Institute, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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162
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Su J, Zhang F, Chong X, Song A, Guan Z, Fang W, Chen F. Genome-wide association study identifies favorable SNP alleles and candidate genes for waterlogging tolerance in chrysanthemums. HORTICULTURE RESEARCH 2019. [PMID: 30729011 DOI: 10.1038/s41438-018-0101-107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Chrysanthemums are sensitive to waterlogging stress, and the development of screening methods for tolerant germplasms or genes and the breeding of tolerant new varieties are of great importance in chrysanthemum breeding. To understand the genetic basis of waterlogging tolerance (WT) in chrysanthemums, we performed a genome-wide association study (GWAS) using 92,811 single nucleotide polymorphisms (SNPs) in a panel of 88 chrysanthemum accessions, including 64 spray cut and 24 disbud chrysanthemums. The results showed that the average MFVW (membership function value of waterlogging) of the disbud type (0.65) was significantly higher than that of the spray type (0.55) at P < 0.05, and the MFVW of the Asian accessions (0.65) was significantly higher than that of the European accessions (0.48) at P < 0.01. The GWAS performed using the general linear model (GLM) and mixed linear model (MLM) identified 137 and 14 SNP loci related to WT, respectively, and 11 associations were commonly predicted. By calculating the phenotypic effect values for 11 common SNP loci, six highly favorable SNP alleles that explained 12.85-21.85% of the phenotypic variations were identified. Furthermore, the dosage-pyramiding effects of the favorable alleles and the significant linear correlations between the numbers of highly favorable alleles and phenotypic values were identified (r 2 = 0.45; P < 0.01). A major SNP locus (Marker6619-75) was converted into a derived cleaved amplified polymorphic sequence (dCAPS) marker that cosegregated with WT with an average efficiency of 78.9%. Finally, four putative candidate genes in the WT were identified via quantitative real-time PCR (qRT-PCR). The results presented in this study provide insights for further research on WT mechanisms and the application of molecular marker-assisted selection (MAS) in chrysanthemum WT breeding programs.
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Affiliation(s)
- Jiangshuo Su
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Fei Zhang
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Xinran Chong
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Aiping Song
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Key Laboratory of Landscape Agriculture, Ministry of Agriculture, 210095 Nanjing, China
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163
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Chialva M, Salvioli di Fossalunga A, Daghino S, Ghignone S, Bagnaresi P, Chiapello M, Novero M, Spadaro D, Perotto S, Bonfante P. Native soils with their microbiotas elicit a state of alert in tomato plants. THE NEW PHYTOLOGIST 2018; 220:1296-1308. [PMID: 29424928 DOI: 10.1111/nph.15014] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 12/19/2017] [Indexed: 05/22/2023]
Abstract
Several studies have investigated soil microbial biodiversity, but understanding of the mechanisms underlying plant responses to soil microbiota remains in its infancy. Here, we focused on tomato (Solanum lycopersicum), testing the hypothesis that plants grown on native soils display different responses to soil microbiotas. Using transcriptomics, proteomics, and biochemistry, we describe the responses of two tomato genotypes (susceptible or resistant to Fusarium oxysporum f. sp. lycopersici) grown on an artificial growth substrate and two native soils (conducive and suppressive to Fusarium). Native soils affected tomato responses by modulating pathways involved in responses to oxidative stress, phenol biosynthesis, lignin deposition, and innate immunity, particularly in the suppressive soil. In tomato plants grown on steam-disinfected soils, total phenols and lignin decreased significantly. The inoculation of a mycorrhizal fungus partly rescued this response locally and systemically. Plants inoculated with the fungal pathogen showed reduced disease symptoms in the resistant genotype in both soils, but the susceptible genotype was partially protected from the pathogen only when grown on the suppressive soil. The 'state of alert' detected in tomatoes reveals novel mechanisms operating in plants in native soils and the soil microbiota appears to be one of the drivers of these plant responses.
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Affiliation(s)
- Matteo Chialva
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, I-10125, Torino, Italy
| | | | - Stefania Daghino
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, I-10125, Torino, Italy
| | - Stefano Ghignone
- Department for Sustainable Plant Protection, Italian National Research Council (CNR), Viale P.A. Mattioli 25, I-10125, Torino, Italy
| | - Paolo Bagnaresi
- Genomics Research Centre CRA-GPG, via S. Protaso, 302, I-29017, Fiorenzuola d'Arda, PC, Italy
| | - Marco Chiapello
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, I-10125, Torino, Italy
| | - Mara Novero
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, I-10125, Torino, Italy
| | - Davide Spadaro
- Department of Agricultural, Forestry and Food Sciences (DiSAFA) and AGROINNOVA - Centre of Competence for the Innovation in the Agroenvironmental Sector, University of Torino, Largo Braccini 2, I-10095, Grugliasco, Italy
| | - Silvia Perotto
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, I-10125, Torino, Italy
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli 25, I-10125, Torino, Italy
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164
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Qian X, Duan T, Sun X, Zheng Y, Wang Y, Hu M, Yao H, Ji N, Lv P, Chen L, Shi M, Guo L, Zhang D. Host genotype strongly influences phyllosphere fungal communities associated with Mussaenda pubescens var. alba (Rubiaceae). FUNGAL ECOL 2018. [DOI: 10.1016/j.funeco.2018.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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165
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Bamba M, Kawaguchi YW, Tsuchimatsu T. Plant adaptation and speciation studied by population genomic approaches. Dev Growth Differ 2018; 61:12-24. [DOI: 10.1111/dgd.12578] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/22/2018] [Accepted: 10/22/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Masaru Bamba
- Department of Biology (Frontier Science Program); Graduate School of Science and Engineering; Chiba University; Chiba Japan
| | - Yawako W. Kawaguchi
- Department of Biology (Frontier Science Program); Graduate School of Science and Engineering; Chiba University; Chiba Japan
| | - Takashi Tsuchimatsu
- Department of Biology; Graduate School of Science; Chiba University; Chiba Japan
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166
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Characterization of microbes and denitrifiers attached to two species of floating plants in the wetlands of Lake Taihu. PLoS One 2018; 13:e0207443. [PMID: 30422988 PMCID: PMC6233912 DOI: 10.1371/journal.pone.0207443] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/31/2018] [Indexed: 11/22/2022] Open
Abstract
Biofilms are often observed at the solid-water interface. The leaves of many floating macrophytes have characteristics of both terrestrial plants and submerged macrophytes, because, in general, their upper and lower surfaces are exposed to air and water, respectively. However, little is known about the biofilms attached to floating plants. We investigated biofilms attached to the leaves, stems and roots of the floating plants Nymphoides peltata (in summer and winter) and Trapa natans (in summer) in the Gonghu Bay of Lake Taihu. Bacteria and algae were major components of the biofilm on the leaves of the two species of plants. In addition, 454 pyrosequencing analysis of bacterial 16S rRNA genes revealed that Proteobacteria was the dominant phylum, followed by Bacteroidetes, Firmicutes, Chloroflexi, Acidobacteria, and Verrucomicrobia. Cluster analysis showed that bacterial communities from the same plant source were clustered into the same group. A total of 677 genera were detected, and 47 genera were shared by all samples. Nitrifiers, including Nitrosomonas, Nitrosococcus and Nitrospira were detected in this study. Seven denitrifying genes (napA, napG, nirS, nirK, cnorB, qnorB and nosZ) were used to detect the abundance of denitrifiers. Genes nirK, nirS cnorB and nosZ were the four most abundant genes in all samples. Our results demonstrated that cultivation of floating plants in water column could enlarge the area for biofilm growth, and biofilms might play an important role in denitrification in eutrophic water.
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167
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Chen C, Huang X, Fang S, Yang H, He M, Zhao Y, Huang L. Contribution of Host Genetics to the Variation of Microbial Composition of Cecum Lumen and Feces in Pigs. Front Microbiol 2018; 9:2626. [PMID: 30429843 PMCID: PMC6220110 DOI: 10.3389/fmicb.2018.02626] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 10/15/2018] [Indexed: 02/01/2023] Open
Abstract
Pigs are a perfect model for studying the interaction between host genetics and gut microbiome due to the high similarity of gastrointestine and digestive system with humans, and the easily controlled feeding conditions. In this study, two pig populations which were raised in uniformed farm conditions and provided with the same commercial formula diet were used as the experimental animals. A systematical investigation of host genetic effect on the gut microbial composition was separately performed in porcine cecum lumen and feces samples through the comparison of microbial composition among full-sibs, half-sibs and unrelated members, heritability estimate (h2), and genome-wide association study (GWAS). The results showed that full-sib members had a higher similarity of microbial composition than unrelated individuals. A significant correlation was observed between the microbial composition-based kinship and the host SNP-based kinship in both populations (P < 9.9 × 10-5). We identified 81 and 67 microbial taxa having h2 > 0.15 in fecal and cecum luminal samples, respectively, including 31 taxa with h2 > 0.15 in both types of samples. GWAS identified 40 and 34 significant associations between host genomic loci and the abundance or presence/absence of bacterial taxa in the fecal and cecum luminal samples. Functional classifications of host candidate genes related to microbial taxa are mainly associated with metabolism, immunity functions and response, and signal transduction. The high similarity of heritable taxa and functional categories of candidate genes among pig, human and mouse suggests the similar mechanism of the host genetic effect on gut microbiome across mammalian species. The results from this study provided another evidence that host genetics contributes significantly to the gut microbiome.
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Affiliation(s)
- Congying Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Xiaochang Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Shaoming Fang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Hui Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Maozhang He
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yuanzhang Zhao
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
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168
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Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota. Nat Commun 2018; 9:2738. [PMID: 30013066 PMCID: PMC6048113 DOI: 10.1038/s41467-018-05122-7] [Citation(s) in RCA: 543] [Impact Index Per Article: 90.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 06/14/2018] [Indexed: 01/16/2023] Open
Abstract
By changing soil properties, plants can modify their growth environment. Although the soil microbiota is known to play a key role in the resulting plant-soil feedbacks, the proximal mechanisms underlying this phenomenon remain unknown. We found that benzoxazinoids, a class of defensive secondary metabolites that are released by roots of cereals such as wheat and maize, alter root-associated fungal and bacterial communities, decrease plant growth, increase jasmonate signaling and plant defenses, and suppress herbivore performance in the next plant generation. Complementation experiments demonstrate that the benzoxazinoid breakdown product 6-methoxy-benzoxazolin-2-one (MBOA), which accumulates in the soil during the conditioning phase, is both sufficient and necessary to trigger the observed phenotypic changes. Sterilization, fungal and bacterial profiling and complementation experiments reveal that MBOA acts indirectly by altering root-associated microbiota. Our results reveal a mechanism by which plants determine the composition of rhizosphere microbiota, plant performance and plant-herbivore interactions of the next generation. Plants can modify soil microbiota through root exudation, but how this process influences plant health in turn is often unclear. Here, Hu et al. show that maize benzoxazinoids released into the soil modify root-associated microbiota and thereby increase leaf defenses of the next plant generation.
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169
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Oyserman BO, Medema MH, Raaijmakers JM. Road MAPs to engineer host microbiomes. Curr Opin Microbiol 2018; 43:46-54. [DOI: 10.1016/j.mib.2017.11.023] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/20/2017] [Accepted: 11/21/2017] [Indexed: 01/07/2023]
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170
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Imboden L, Afton D, Trail F. Surface interactions of Fusarium graminearum on barley. MOLECULAR PLANT PATHOLOGY 2018; 19:1332-1342. [PMID: 28940853 PMCID: PMC6638126 DOI: 10.1111/mpp.12616] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 08/22/2017] [Accepted: 09/18/2017] [Indexed: 05/10/2023]
Abstract
The filamentous fungus Fusarium graminearum, a devastating pathogen of barley (Hordeum vulgare L.), produces mycotoxins that pose a health hazard. To investigate the surface interactions of F. graminearum on barley, we focused on barley florets, as the most important infection site leading to grain contamination. The fungus interacted with silica-accumulating cells (trichomes and silica/cork cell pairs) on the host surface. We identified variation in trichome-type cells between two-row and six-row barley, and in the role of specific epidermal cells in the ingress of F. graminearum into barley florets. Prickle-type trichomes functioned to trap conidia and were sites of fungal penetration. Infections of more mature florets supported the spread of hyphae into the vascular bundles, whereas younger florets did not show this spread. These differences related directly to the timing and location of increases in silica content during maturation. Focal accumulation of cellulose in infected paleae of two-row and six-row barley indicated that the response is in part linked to trichome type. Overall, silica-accumulating epidermal cells had an expanded role in barley, serving to trap conidia, provide sites for fungal ingress and initiate resistance responses, suggesting a role for silica in pathogen establishment.
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Affiliation(s)
- Lori Imboden
- Department of Plant BiologyMichigan State UniversityEast LansingMI 48824USA
| | - Drew Afton
- Department of Plant BiologyMichigan State UniversityEast LansingMI 48824USA
| | - Frances Trail
- Department of Plant BiologyMichigan State UniversityEast LansingMI 48824USA
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMI 48824USA
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171
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In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana. ISME JOURNAL 2018; 12:2024-2038. [PMID: 29849170 DOI: 10.1038/s41396-018-0152-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/21/2018] [Accepted: 04/29/2018] [Indexed: 12/21/2022]
Abstract
A current challenge in microbial pathogenesis is to identify biological control agents that may prevent and/or limit host invasion by microbial pathogens. In natura, hosts are often infected by multiple pathogens. However, most of the current studies have been performed under laboratory controlled conditions and by taking into account the interaction between a single commensal species and a single pathogenic species. The next step is therefore to explore the relationships between host-microbial communities (microbiota) and microbial members with potential pathogenic behavior (pathobiota) in a realistic ecological context. In the present study, we investigated such relationships within root-associated and leaf-associated bacterial communities of 163 ecologically contrasted Arabidopsis thaliana populations sampled across two seasons in southwest of France. In agreement with the theory of the invasion paradox, we observed a significant humped-back relationship between microbiota and pathobiota α-diversity that was robust between both seasons and plant organs. In most populations, we also observed a strong dynamics of microbiota composition between seasons. Accordingly, the potential pathobiota composition was explained by combinations of season-specific microbiota operational taxonomic units. This result suggests that the potential biomarkers controlling pathogen's invasion are highly dynamic.
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172
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Wang J, Chen L, Zhao N, Xu X, Xu Y, Zhu B. Of genes and microbes: solving the intricacies in host genomes. Protein Cell 2018; 9:446-461. [PMID: 29611114 PMCID: PMC5960464 DOI: 10.1007/s13238-018-0532-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 02/28/2018] [Indexed: 12/14/2022] Open
Abstract
Microbiome research is a quickly developing field in biomedical research, and we have witnessed its potential in understanding the physiology, metabolism and immunology, its critical role in understanding the health and disease of the host, and its vast capacity in disease prediction, intervention and treatment. However, many of the fundamental questions still need to be addressed, including the shaping forces of microbial diversity between individuals and across time. Microbiome research falls into the classical nature vs. nurture scenario, such that host genetics shape part of the microbiome, while environmental influences change the original course of microbiome development. In this review, we focus on the nature, i.e., the genetic part of the equation, and summarize the recent efforts in understanding which parts of the genome, especially the human and mouse genome, play important roles in determining the composition and functions of microbial communities, primarily in the gut but also on the skin. We aim to present an overview of different approaches in studying the intricate relationships between host genetic variations and microbes, its underlying philosophy and methodology, and we aim to highlight a few key discoveries along this exploration, as well as current pitfalls. More evidence and results will surely appear in upcoming studies, and the accumulating knowledge will lead to a deeper understanding of what we could finally term a "hologenome", that is, the organized, closely interacting genome of the host and the microbiome.
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Affiliation(s)
- Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China.
| | - Liang Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China
| | - Na Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China
| | - Xizhan Xu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yakun Xu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China.
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173
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Hassani MA, Durán P, Hacquard S. Microbial interactions within the plant holobiont. MICROBIOME 2018; 6:58. [PMID: 29587885 PMCID: PMC5870681 DOI: 10.1186/s40168-018-0445-0] [Citation(s) in RCA: 501] [Impact Index Per Article: 83.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/13/2018] [Indexed: 05/09/2023]
Abstract
Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a "holobiont." Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments. Reductionist approaches conducted under laboratory conditions have been critical to decipher the strategies used by specific microbes to cooperate and compete within or outside plant tissues. Nonetheless, our understanding of these microbial interactions in shaping more complex plant-associated microbial communities, along with their relevance for host health in a more natural context, remains sparse. Using examples obtained from reductionist and community-level approaches, we discuss the fundamental role of microbe-microbe interactions (prokaryotes and micro-eukaryotes) for microbial community structure and plant health. We provide a conceptual framework illustrating that interactions among microbiota members are critical for the establishment and the maintenance of host-microbial homeostasis.
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Affiliation(s)
- M Amine Hassani
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Paloma Durán
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
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174
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175
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Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice. PLoS Biol 2018; 16:e2003862. [PMID: 29474469 PMCID: PMC5841827 DOI: 10.1371/journal.pbio.2003862] [Citation(s) in RCA: 209] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 03/07/2018] [Accepted: 02/02/2018] [Indexed: 02/01/2023] Open
Abstract
Bacterial communities associated with roots impact the health and nutrition of the host plant. The dynamics of these microbial assemblies over the plant life cycle are, however, not well understood. Here, we use dense temporal sampling of 1,510 samples from root spatial compartments to characterize the bacterial and archaeal components of the root-associated microbiota of field grown rice (Oryza sativa) over the course of 3 consecutive growing seasons, as well as 2 sites in diverse geographic regions. The root microbiota was found to be highly dynamic during the vegetative phase of plant growth and then stabilized compositionally for the remainder of the life cycle. Bacterial and archaeal taxa conserved between field sites were defined as predictive features of rice plant age by modeling using a random forest approach. The age-prediction models revealed that drought-stressed plants have developmentally immature microbiota compared to unstressed plants. Further, by using genotypes with varying developmental rates, we show that shifts in the microbiome are correlated with rates of developmental transitions rather than age alone, such that different microbiota compositions reflect juvenile and adult life stages. These results suggest a model for successional dynamics of the root-associated microbiota over the plant life cycle. Plant roots are colonized by complex communities of bacterial and archaeal microbiota from the soil, with the potential to affect plant nutrition and fitness. Although root-associated microbes are known to have the potential to be utilized to promote crop productivity, their exploitation has been hindered by a lack of understanding of the compositional dynamics of these communities. Here we investigate temporal changes in the root-associated bacterial and archaeal communities throughout the plant life cycle in field-grown rice over multiple seasons and locations. Our results indicate that root microbiota composition varies with both chronological age and the developmental stage of the plants. We find that a major compositional shift correlates with the transition to reproductive growth, suggestive of distinct root microbiota associations for the juvenile and adult plant phases. The results from this study highlight dynamic relationships between plant growth and associated microbiota that should be considered in strategies for the successful manipulation of microbial communities to enhance crop performance.
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176
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Aydogan EL, Moser G, Müller C, Kämpfer P, Glaeser SP. Long-Term Warming Shifts the Composition of Bacterial Communities in the Phyllosphere of Galium album in a Permanent Grassland Field-Experiment. Front Microbiol 2018; 9:144. [PMID: 29487575 PMCID: PMC5816784 DOI: 10.3389/fmicb.2018.00144] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 01/23/2018] [Indexed: 11/13/2022] Open
Abstract
Global warming is currently a much discussed topic with as yet largely unexplored consequences for agro-ecosystems. Little is known about the warming effect on the bacterial microbiota inhabiting the plant surface (phyllosphere), which can have a strong impact on plant growth and health, as well as on plant diseases and colonization by human pathogens. The aim of this study was to investigate the effect of moderate surface warming on the diversity and composition of the bacterial leaf microbiota of the herbaceous plant Galium album. Leaves were collected from four control and four surface warmed (+2°C) plots located at the field site of the Environmental Monitoring and Climate Impact Research Station Linden in Germany over a 6-year period. Warming had no effect on the concentration of total number of cells attached to the leaf surface as counted by Sybr Green I staining after detachment, but changes in the diversity and phylogenetic composition of the bacterial leaf microbiota analyzed by bacterial 16S rRNA gene Illumina amplicon sequencing were observed. The bacterial phyllosphere microbiota were dominated by Proteobacteria, Bacteroidetes, and Actinobacteria. Warming caused a significant higher relative abundance of members of the Gammaproteobacteria, Actinobacteria, and Firmicutes, and a lower relative abundance of members of the Alphaproteobacteria and Bacteroidetes. Plant beneficial bacteria like Sphingomonas spp. and Rhizobium spp. occurred in significantly lower relative abundance in leaf samples of warmed plots. In contrast, several members of the Enterobacteriaceae, especially Enterobacter and Erwinia, and other potential plant or human pathogenic genera such as Acinetobacter and insect-associated Buchnera and Wolbachia spp. occurred in higher relative abundances in the phyllosphere samples from warmed plots. This study showed for the first time the long-term impact of moderate (+2°C) surface warming on the phyllosphere microbiota on plants. A reduction of beneficial bacteria and an enhancement of potential pathogenic bacteria in the phyllosphere of plants may indicate that this aspect of the ecosystem which has been largely neglected up till now, can be a potential risk for pathogen transmission in agro-ecosystems in the near future.
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Affiliation(s)
- Ebru L. Aydogan
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Gerald Moser
- Institute for Plant Ecology, Justus Liebig University Giessen, Giessen, Germany
| | - Christoph Müller
- Institute for Plant Ecology, Justus Liebig University Giessen, Giessen, Germany
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Peter Kämpfer
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Stefanie P. Glaeser
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
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177
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Bacete L, Mélida H, Miedes E, Molina A. Plant cell wall-mediated immunity: cell wall changes trigger disease resistance responses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:614-636. [PMID: 29266460 DOI: 10.1111/tpj.13807] [Citation(s) in RCA: 274] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/07/2017] [Accepted: 12/14/2017] [Indexed: 05/18/2023]
Abstract
Plants have evolved a repertoire of monitoring systems to sense plant morphogenesis and to face environmental changes and threats caused by different attackers. These systems integrate different signals into overreaching triggering pathways which coordinate developmental and defence-associated responses. The plant cell wall, a dynamic and complex structure surrounding every plant cell, has emerged recently as an essential component of plant monitoring systems, thus expanding its function as a passive defensive barrier. Plants have a dedicated mechanism for maintaining cell wall integrity (CWI) which comprises a diverse set of plasma membrane-resident sensors and pattern recognition receptors (PRRs). The PRRs perceive plant-derived ligands, such as peptides or wall glycans, known as damage-associated molecular patterns (DAMPs). These DAMPs function as 'danger' alert signals activating DAMP-triggered immunity (DTI), which shares signalling components and responses with the immune pathways triggered by non-self microbe-associated molecular patterns that mediate disease resistance. Alteration of CWI by impairment of the expression or activity of proteins involved in cell wall biosynthesis and/or remodelling, as occurs in some plant cell wall mutants, or by wall damage due to colonization by pathogens/pests, activates specific defensive and growth responses. Our current understanding of how these alterations of CWI are perceived by the wall monitoring systems is scarce and few plant sensors/PRRs and DAMPs have been characterized. The identification of these CWI sensors and PRR-DAMP pairs will help us to understand the immune functions of the wall monitoring system, and might allow the breeding of crop varieties and the design of agricultural strategies that would enhance crop disease resistance.
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Affiliation(s)
- Laura Bacete
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, 28040, Madrid, Spain
| | - Hugo Mélida
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Eva Miedes
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, 28040, Madrid, Spain
| | - Antonio Molina
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, 28040, Madrid, Spain
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178
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Peredo EL, Simmons SL. Leaf-FISH: Microscale Imaging of Bacterial Taxa on Phyllosphere. Front Microbiol 2018; 8:2669. [PMID: 29375531 PMCID: PMC5767230 DOI: 10.3389/fmicb.2017.02669] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/21/2017] [Indexed: 11/13/2022] Open
Abstract
Molecular methods for microbial community characterization have uncovered environmental and plant-associated factors shaping phyllosphere communities. Variables undetectable using bulk methods can play an important role in shaping plant-microbe interactions. Microscale analysis of bacterial dynamics in the phyllosphere requires imaging techniques specially adapted to the high autoflouresence and 3-D structure of the leaf surface. We present an easily-transferable method (Leaf-FISH) to generate high-resolution tridimensional images of leaf surfaces that allows simultaneous visualization of multiple bacterial taxa in a structurally informed context, using taxon-specific fluorescently labeled oligonucleotide probes. Using a combination of leaf pretreatments coupled with spectral imaging confocal microscopy, we demonstrate the successful imaging bacterial taxa at the genus level on cuticular and subcuticular leaf areas. Our results confirm that different bacterial species, including closely related isolates, colonize distinct microhabitats in the leaf. We demonstrate that highly related Methylobacterium species have distinct colonization patterns that could not be predicted by shared physiological traits, such as carbon source requirements or phytohormone production. High-resolution characterization of microbial colonization patterns is critical for an accurate understanding of microbe-microbe and microbe-plant interactions, and for the development of foliar bacteria as plant-protective agents.
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Affiliation(s)
- Elena L Peredo
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, MA, United States
| | - Sheri L Simmons
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, MA, United States
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179
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Dijkhuizen LW, Brouwer P, Bolhuis H, Reichart GJ, Koppers N, Huettel B, Bolger AM, Li FW, Cheng S, Liu X, Wong GKS, Pryer K, Weber A, Bräutigam A, Schluepmann H. Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N 2 but may denitrify. THE NEW PHYTOLOGIST 2018. [PMID: 26680538 DOI: 10.1111/nph] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Dinitrogen fixation by Nostoc azollae residing in specialized leaf pockets supports prolific growth of the floating fern Azolla filiculoides. To evaluate contributions by further microorganisms, the A. filiculoides microbiome and nitrogen metabolism in bacteria persistently associated with Azolla ferns were characterized. A metagenomic approach was taken complemented by detection of N2 O released and nitrogen isotope determinations of fern biomass. Ribosomal RNA genes in sequenced DNA of natural ferns, their enriched leaf pockets and water filtrate from the surrounding ditch established that bacteria of A. filiculoides differed entirely from surrounding water and revealed species of the order Rhizobiales. Analyses of seven cultivated Azolla species confirmed persistent association with Rhizobiales. Two distinct nearly full-length Rhizobiales genomes were identified in leaf-pocket-enriched samples from ditch grown A. filiculoides. Their annotation revealed genes for denitrification but not N2 -fixation. 15 N2 incorporation was active in ferns with N. azollae but not in ferns without. N2 O was not detectably released from surface-sterilized ferns with the Rhizobiales. N2 -fixing N. azollae, we conclude, dominated the microbiome of Azolla ferns. The persistent but less abundant heterotrophic Rhizobiales bacteria possibly contributed to lowering O2 levels in leaf pockets but did not release detectable amounts of the strong greenhouse gas N2 O.
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Affiliation(s)
- Laura W Dijkhuizen
- Molecular Plant Physiology Department, Utrecht University, Padualaan 8, Utrecht, 3584CH, the Netherlands
| | - Paul Brouwer
- Molecular Plant Physiology Department, Utrecht University, Padualaan 8, Utrecht, 3584CH, the Netherlands
| | - Henk Bolhuis
- Department of Marine Microbiology and Biogeochemistry, Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Hoorn, 1797SZ, the Netherlands
| | - Gert-Jan Reichart
- Department of Earth Sciences, Utrecht University, Utrecht, 3508TA, the Netherlands
| | - Nils Koppers
- Department of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, 40225, Germany
| | - Bruno Huettel
- Max Planck Institute for Plant Breeding ADIS/DNA Core Facility, Cologne, 50829, Germany
| | - Anthony M Bolger
- Institute of Botany and Molecular Genetics IBMG, IRWTH Aachen University, 52074, Aachen, Germany
| | - Fay-Wei Li
- Department of Biology, Duke University, Durham, NC, 27708, USA
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA
| | - Shifeng Cheng
- Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China
| | - Xin Liu
- Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China
| | - Gane Ka-Shu Wong
- Beijing Genomics Institute-Shenzhen, Shenzhen, 518083, China
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Kathleen Pryer
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Andreas Weber
- Department of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, 40225, Germany
| | - Andrea Bräutigam
- Department of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, 40225, Germany
| | - Henriette Schluepmann
- Molecular Plant Physiology Department, Utrecht University, Padualaan 8, Utrecht, 3584CH, the Netherlands
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180
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Sergaki C, Lagunas B, Lidbury I, Gifford ML, Schäfer P. Challenges and Approaches in Microbiome Research: From Fundamental to Applied. FRONTIERS IN PLANT SCIENCE 2018; 9:1205. [PMID: 30174681 PMCID: PMC6107787 DOI: 10.3389/fpls.2018.01205] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/26/2018] [Indexed: 05/07/2023]
Abstract
We face major agricultural challenges that remain a threat for global food security. Soil microbes harbor enormous potentials to provide sustainable and economically favorable solutions that could introduce novel approaches to improve agricultural practices and, hence, crop productivity. In this review we give an overview regarding the current state-of-the-art of microbiome research by discussing new technologies and approaches. We also provide insights into fundamental microbiome research that aim to provide a deeper understanding of the dynamics within microbial communities, as well as their interactions with different plant hosts and the environment. We aim to connect all these approaches with potential applications and reflect how we can use microbial communities in modern agricultural systems to realize a more customized and sustainable use of valuable resources (e.g., soil).
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Affiliation(s)
- Chrysi Sergaki
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- *Correspondence: Chrysi Sergaki,
| | - Beatriz Lagunas
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Ian Lidbury
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Miriam L. Gifford
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, United Kingdom
| | - Patrick Schäfer
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, United Kingdom
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181
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Dijkhuizen LW, Brouwer P, Bolhuis H, Reichart G, Koppers N, Huettel B, Bolger AM, Li F, Cheng S, Liu X, Wong GK, Pryer K, Weber A, Bräutigam A, Schluepmann H. Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N 2 but may denitrify. THE NEW PHYTOLOGIST 2018; 217:453-466. [PMID: 29084347 PMCID: PMC5901025 DOI: 10.1111/nph.14843] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 09/05/2017] [Indexed: 05/18/2023]
Abstract
Dinitrogen fixation by Nostoc azollae residing in specialized leaf pockets supports prolific growth of the floating fern Azolla filiculoides. To evaluate contributions by further microorganisms, the A. filiculoides microbiome and nitrogen metabolism in bacteria persistently associated with Azolla ferns were characterized. A metagenomic approach was taken complemented by detection of N2 O released and nitrogen isotope determinations of fern biomass. Ribosomal RNA genes in sequenced DNA of natural ferns, their enriched leaf pockets and water filtrate from the surrounding ditch established that bacteria of A. filiculoides differed entirely from surrounding water and revealed species of the order Rhizobiales. Analyses of seven cultivated Azolla species confirmed persistent association with Rhizobiales. Two distinct nearly full-length Rhizobiales genomes were identified in leaf-pocket-enriched samples from ditch grown A. filiculoides. Their annotation revealed genes for denitrification but not N2 -fixation. 15 N2 incorporation was active in ferns with N. azollae but not in ferns without. N2 O was not detectably released from surface-sterilized ferns with the Rhizobiales. N2 -fixing N. azollae, we conclude, dominated the microbiome of Azolla ferns. The persistent but less abundant heterotrophic Rhizobiales bacteria possibly contributed to lowering O2 levels in leaf pockets but did not release detectable amounts of the strong greenhouse gas N2 O.
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Affiliation(s)
- Laura W. Dijkhuizen
- Molecular Plant Physiology DepartmentUtrecht UniversityPadualaan 8Utrecht3584CHthe Netherlands
| | - Paul Brouwer
- Molecular Plant Physiology DepartmentUtrecht UniversityPadualaan 8Utrecht3584CHthe Netherlands
| | - Henk Bolhuis
- Department of Marine Microbiology and BiogeochemistryNetherlands Institute for Sea Research (NIOZ)Utrecht UniversityDen Hoorn1797SZthe Netherlands
| | - Gert‐Jan Reichart
- Department of Earth SciencesUtrecht UniversityUtrecht3508TAthe Netherlands
| | - Nils Koppers
- Department of Plant BiochemistryCluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorf40225Germany
| | - Bruno Huettel
- Max Planck Institute for Plant Breeding ADIS/DNA Core FacilityCologne50829Germany
| | - Anthony M. Bolger
- Institute of Botany and Molecular Genetics IBMGIRWTH Aachen University52074AachenGermany
| | - Fay‐Wei Li
- Department of BiologyDuke UniversityDurhamNC27708USA
- Boyce Thompson Institute for Plant ResearchCornell UniversityIthacaNY14853USA
| | - Shifeng Cheng
- Beijing Genomics Institute‐ShenzhenShenzhen518083China
| | - Xin Liu
- Beijing Genomics Institute‐ShenzhenShenzhen518083China
| | - Gane Ka‐Shu Wong
- Beijing Genomics Institute‐ShenzhenShenzhen518083China
- Department of Biological SciencesUniversity of AlbertaEdmontonABT6G 2E9Canada
| | | | - Andreas Weber
- Department of Plant BiochemistryCluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorf40225Germany
| | - Andrea Bräutigam
- Department of Plant BiochemistryCluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorf40225Germany
| | - Henriette Schluepmann
- Molecular Plant Physiology DepartmentUtrecht UniversityPadualaan 8Utrecht3584CHthe Netherlands
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182
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Chen C, Huang X, Fang S, Yang H, He M, Zhao Y, Huang L. Contribution of Host Genetics to the Variation of Microbial Composition of Cecum Lumen and Feces in Pigs. Front Microbiol 2018. [PMID: 30429843 DOI: 10.3389/fmicb.2018.02626/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
Pigs are a perfect model for studying the interaction between host genetics and gut microbiome due to the high similarity of gastrointestine and digestive system with humans, and the easily controlled feeding conditions. In this study, two pig populations which were raised in uniformed farm conditions and provided with the same commercial formula diet were used as the experimental animals. A systematical investigation of host genetic effect on the gut microbial composition was separately performed in porcine cecum lumen and feces samples through the comparison of microbial composition among full-sibs, half-sibs and unrelated members, heritability estimate (h 2), and genome-wide association study (GWAS). The results showed that full-sib members had a higher similarity of microbial composition than unrelated individuals. A significant correlation was observed between the microbial composition-based kinship and the host SNP-based kinship in both populations (P < 9.9 × 10-5). We identified 81 and 67 microbial taxa having h 2 > 0.15 in fecal and cecum luminal samples, respectively, including 31 taxa with h 2 > 0.15 in both types of samples. GWAS identified 40 and 34 significant associations between host genomic loci and the abundance or presence/absence of bacterial taxa in the fecal and cecum luminal samples. Functional classifications of host candidate genes related to microbial taxa are mainly associated with metabolism, immunity functions and response, and signal transduction. The high similarity of heritable taxa and functional categories of candidate genes among pig, human and mouse suggests the similar mechanism of the host genetic effect on gut microbiome across mammalian species. The results from this study provided another evidence that host genetics contributes significantly to the gut microbiome.
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Affiliation(s)
- Congying Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Xiaochang Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Shaoming Fang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Hui Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Maozhang He
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yuanzhang Zhao
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
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183
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Colla G, Hoagland L, Ruzzi M, Cardarelli M, Bonini P, Canaguier R, Rouphael Y. Biostimulant Action of Protein Hydrolysates: Unraveling Their Effects on Plant Physiology and Microbiome. FRONTIERS IN PLANT SCIENCE 2017; 8:2202. [PMID: 29312427 PMCID: PMC5744479 DOI: 10.3389/fpls.2017.02202] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/14/2017] [Indexed: 05/18/2023]
Abstract
Plant-derived protein hydrolysates (PHs) have gained prominence as plant biostimulants because of their potential to increase the germination, productivity and quality of a wide range of horticultural and agronomic crops. Application of PHs can also alleviate the negative effects of abiotic plant stress due to salinity, drought and heavy metals. Recent studies aimed at uncovering the mechanisms regulating these beneficial effects indicate that PHs could be directly affecting plants by stimulating carbon and nitrogen metabolism, and interfering with hormonal activity. Indirect effects could also play a role as PHs could enhance nutrient availability in plant growth substrates, and increase nutrient uptake and nutrient-use efficiency in plants. Moreover, the beneficial effects of PHs also could be due to the stimulation of plant microbiomes. Plants are colonized by an abundant and diverse assortment of microbial taxa that can help plants acquire nutrients and water and withstand biotic and abiotic stress. The substrates provided by PHs, such as amino acids, could provide an ideal food source for these plant-associated microbes. Indeed, recent studies have provided evidence that plant microbiomes are modified by the application of PHs, supporting the hypothesis that PHs might be acting, at least in part, via changes in the composition and activity of these microbial communities. Application of PHs has great potential to meet the twin challenges of a feeding a growing population while minimizing agriculture's impact on human health and the environment. However, to fully realize the potential of PHs, further studies are required to shed light on the mechanisms conferring the beneficial effects of these products, as well as identify product formulations and application methods that optimize benefits under a range of agro-ecological conditions.
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Affiliation(s)
- Giuseppe Colla
- Department of Agricultural and Forestry Sciences, University of Tuscia, Viterbo, Italy
| | - Lori Hoagland
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
| | - Maurizio Ruzzi
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy
| | - Mariateresa Cardarelli
- Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Centro di Ricerca Orticoltura e Florovivaismo, Pontecagnano, Italy
| | | | | | - Youssef Rouphael
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
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184
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Wu Q, Cui K, Lin J, Zhu Y, Xu Y. Urea production by yeasts other than Saccharomyces in food fermentation. FEMS Yeast Res 2017; 17:4411803. [PMID: 29040547 DOI: 10.1093/femsyr/fox072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/26/2017] [Indexed: 11/15/2022] Open
Abstract
Urea is an important intermediate in the synthesis of carcinogenic ethyl carbamate in various food fermentations. Identifying urea-producing microorganisms can help control or reduce ethyl carbamate production. Using Chinese liquor fermentation as a model system, we identified the yeasts responsible for urea production. Urea production was positively correlated to the yeast population (R = 0.523, P = 0.045), and using high-throughput sequencing, we identified 26 yeast species. Partial least squares regression and correlation analysis indicated that Wickerhamomyces anomalus was the most important yeast to produce urea (variable importance plot = 1.927; R = 0.719, P = 0.002). Besides, we found that in W. anomalus the CAR1 gene (responsible for urea production) was 67% identical to that of Saccharomyces cerevisiae. Wickerhamomyces anomalus produced more urea (910.0 μg L-1) than S. cerevisiae (300.1 μg L-1). Moreover, urea production increased to 1261.2 μg L-1 when the two yeasts were co-cultured in a simulated fermentation, where the transcription activity of the CAR1 gene increased by 140% in W. anomalus and decreased by 40% in S. cerevisiae. Our findings confirm that a yeast other than Saccharomyces, namely W. anomalus, contributes more to urea formation in a simulated sorghum fermentation. These findings provide the basis for strategies to control or reduce ethyl carbamate formation.
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Affiliation(s)
- Qun Wu
- State Key Laboratory of Food Science and Technology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, Synergetic Innovation Centre of Food Safety and Nutrition, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Kaixiang Cui
- State Key Laboratory of Food Science and Technology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, Synergetic Innovation Centre of Food Safety and Nutrition, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jianchun Lin
- State Key Laboratory of Food Science and Technology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, Synergetic Innovation Centre of Food Safety and Nutrition, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yang Zhu
- Bioprocess Engineering, Wageningen University and Research, PO Box 16, 6700 AA Wageningen, Netherlands
| | - Yan Xu
- State Key Laboratory of Food Science and Technology, The Key Laboratory of Industrial Biotechnology, Ministry of Education, Synergetic Innovation Centre of Food Safety and Nutrition, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
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185
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Jacoby R, Peukert M, Succurro A, Koprivova A, Kopriva S. The Role of Soil Microorganisms in Plant Mineral Nutrition-Current Knowledge and Future Directions. FRONTIERS IN PLANT SCIENCE 2017; 8:1617. [PMID: 28974956 PMCID: PMC5610682 DOI: 10.3389/fpls.2017.01617] [Citation(s) in RCA: 351] [Impact Index Per Article: 50.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 09/04/2017] [Indexed: 05/18/2023]
Abstract
In their natural environment, plants are part of a rich ecosystem including numerous and diverse microorganisms in the soil. It has been long recognized that some of these microbes, such as mycorrhizal fungi or nitrogen fixing symbiotic bacteria, play important roles in plant performance by improving mineral nutrition. However, the full range of microbes associated with plants and their potential to replace synthetic agricultural inputs has only recently started to be uncovered. In the last few years, a great progress has been made in the knowledge on composition of rhizospheric microbiomes and their dynamics. There is clear evidence that plants shape microbiome structures, most probably by root exudates, and also that bacteria have developed various adaptations to thrive in the rhizospheric niche. The mechanisms of these interactions and the processes driving the alterations in microbiomes are, however, largely unknown. In this review, we focus on the interaction of plants and root associated bacteria enhancing plant mineral nutrition, summarizing the current knowledge in several research fields that can converge to improve our understanding of the molecular mechanisms underpinning this phenomenon.
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Affiliation(s)
| | | | | | | | - Stanislav Kopriva
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of CologneCologne, Germany
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186
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Morella NM, Koskella B. The Value of a Comparative Approach to Understand the Complex Interplay between Microbiota and Host Immunity. Front Immunol 2017; 8:1114. [PMID: 28959258 PMCID: PMC5603614 DOI: 10.3389/fimmu.2017.01114] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 08/24/2017] [Indexed: 01/17/2023] Open
Abstract
The eukaryote immune system evolved and continues to evolve within a microbial world, and as such is critically shaped by-and in some cases even reliant upon-the presence of host-associated microbial species. There are clear examples of adaptations that allow the host to simultaneously tolerate and/or promote growth of symbiotic microbiota while protecting itself against pathogens, but the relationship between immunity and the microbiome reaches far beyond simple recognition and includes complex cross talk between host and microbe as well as direct microbiome-mediated protection against pathogens. Here, we present a broad but brief overview of how the microbiome is controlled by and interacts with diverse immune systems, with the goal of identifying questions that can be better addressed by taking a comparative approach across plants and animals and different types of immunity. As two key examples of such an approach, we focus on data examining the importance of early exposure on microbiome tolerance and immune system development and function, and the importance of transmission among hosts in shaping the potential coevolution between, and long-term stability of, host-microbiome associations. Then, by comparing existing evidence across short-lived plants, mouse model systems and humans, and insects, we highlight areas of microbiome research that are strong in some systems and absent in others with the hope of guiding future research that will allow for broad-scale comparisons moving forward. We argue that such an approach will not only help with identification of generalities in host-microbiome-immune interactions but also improve our understanding of the role of the microbiome in host health.
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Affiliation(s)
- Norma M. Morella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
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187
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Karasov TL, Barrett L, Hershberg R, Bergelson J. Similar levels of gene content variation observed for Pseudomonas syringae populations extracted from single and multiple host species. PLoS One 2017; 12:e0184195. [PMID: 28880925 PMCID: PMC5589212 DOI: 10.1371/journal.pone.0184195] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 08/18/2017] [Indexed: 12/22/2022] Open
Abstract
Bacterial strains of the same species collected from different hosts frequently exhibit differences in gene content. In the ubiquitous plant pathogen Pseudomonas syringae, more than 30% of genes encoded by each strain are not conserved among strains colonizing other host species. Although they are often implicated in host specificity, the role of this large fraction of the genome in host-specific adaptation is largely unexplored. Here, we sought to relate variation in gene content between strains infecting different species to variation that persists between strains on the same host. We fully sequenced a collection of P. syringae strains collected from wild Arabidopsis thaliana populations in the Midwestern United States. We then compared patterns of variation observed in gene content within these A. thaliana-isolated strains to previously published P. syringae sequence from strains collected on a diversity of crop species. We find that strains collected from the same host, A. thaliana, differ in gene content by 21%, 2/3 the level of gene content variation observed across strains collected from different hosts. Furthermore, the frequency with which specific genes are present among strains collected within the same host and among strains collected from different hosts is highly correlated. This implies that most gene content variation is maintained irrespective of host association. At the same time, we identify specific genes whose presence is important for P. syringae's ability to flourish within A. thaliana. Specifically, the A. thaliana strains uniquely share a genomic island encoding toxins active against plants and surrounding microbes, suggesting a role for microbe-microbe interactions in dictating the abundance within this host. Overall, our results demonstrate that while variation in the presence of specific genes can affect the success of a pathogen within its host, the majority of gene content variation is not strongly associated with patterns of host use.
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Affiliation(s)
- Talia L. Karasov
- Committee On Genetics Genomics & Systems Biology, University of Chicago, Chicago, Illinois, United States of America
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Luke Barrett
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
- CSIRO Agriculture, Canberra, ACT 2601, Australia
| | - Ruth Hershberg
- Department of Genetics, the Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Joy Bergelson
- Committee On Genetics Genomics & Systems Biology, University of Chicago, Chicago, Illinois, United States of America
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
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188
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Bowen JL, Kearns PJ, Byrnes JEK, Wigginton S, Allen WJ, Greenwood M, Tran K, Yu J, Cronin JT, Meyerson LA. Lineage overwhelms environmental conditions in determining rhizosphere bacterial community structure in a cosmopolitan invasive plant. Nat Commun 2017; 8:433. [PMID: 28874666 PMCID: PMC5585233 DOI: 10.1038/s41467-017-00626-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 07/13/2017] [Indexed: 02/01/2023] Open
Abstract
Plant-microbe interactions play crucial roles in species invasions but are rarely investigated at the intraspecific level. Here, we study these interactions in three lineages of a globally distributed plant, Phragmites australis. We use field surveys and a common garden experiment to analyze bacterial communities in the rhizosphere of P. australis stands from native, introduced, and Gulf lineages to determine lineage-specific controls on rhizosphere bacteria. We show that within-lineage bacterial communities are similar, but are distinct among lineages, which is consistent with our results in a complementary common garden experiment. Introduced P. australis rhizosphere bacterial communities have lower abundances of pathways involved in antimicrobial biosynthesis and degradation, suggesting a lower exposure to enemy attack than native and Gulf lineages. However, lineage and not rhizosphere bacterial communities dictate individual plant growth in the common garden experiment. We conclude that lineage is crucial for determination of both rhizosphere bacterial communities and plant fitness.Environmental factors often outweigh host heritable factors in structuring host-associated microbiomes. Here, Bowen et al. show that host lineage is crucial for determination of rhizosphere bacterial communities in Phragmites australis, a globally distributed invasive plant.
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Affiliation(s)
- Jennifer L Bowen
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, 430 Nahant Road, Nahant, MA, 01908, USA.
| | - Patrick J Kearns
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, 430 Nahant Road, Nahant, MA, 01908, USA
| | - Jarrett E K Byrnes
- University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA, 02125, USA
| | - Sara Wigginton
- Department of Natural Resources Science, University of Rhode Island, Woodward Hall, 9 East Alumni Avenue, Kingston, RI, 02881, USA
| | - Warwick J Allen
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
- The Bio-Protection Research Centre, Lincoln University, PO Box 84, Lincoln, 7647, New Zealand
| | - Michael Greenwood
- University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA, 02125, USA
| | - Khang Tran
- University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA, 02125, USA
| | - Jennifer Yu
- University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA, 02125, USA
| | - James T Cronin
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA, 70803, USA
| | - Laura A Meyerson
- Department of Natural Resources Science, University of Rhode Island, Woodward Hall, 9 East Alumni Avenue, Kingston, RI, 02881, USA
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189
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Hacquard S, Spaepen S, Garrido-Oter R, Schulze-Lefert P. Interplay Between Innate Immunity and the Plant Microbiota. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:565-589. [PMID: 28645232 DOI: 10.1146/annurev-phyto-080516-035623] [Citation(s) in RCA: 233] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The innate immune system of plants recognizes microbial pathogens and terminates their growth. However, recent findings suggest that at least one layer of this system is also engaged in cooperative plant-microbe interactions and influences host colonization by beneficial microbial communities. This immune layer involves sensing of microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs) that initiate quantitative immune responses to control host-microbial load, whereas diversification of MAMPs and PRRs emerges as a mechanism that locally sculpts microbial assemblages in plant populations. This suggests a more complex microbial management role of the innate immune system for controlled accommodation of beneficial microbes and in pathogen elimination. The finding that similar molecular strategies are deployed by symbionts and pathogens to dampen immune responses is consistent with this hypothesis but implies different selective pressures on the immune system due to contrasting outcomes on plant fitness. The reciprocal interplay between microbiota and the immune system likely plays a critical role in shaping beneficial plant-microbiota combinations and maintaining microbial homeostasis.
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Affiliation(s)
- Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
| | - Stijn Spaepen
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
| | - Ruben Garrido-Oter
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
- Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany;
- Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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190
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Finkel OM, Castrillo G, Herrera Paredes S, Salas González I, Dangl JL. Understanding and exploiting plant beneficial microbes. CURRENT OPINION IN PLANT BIOLOGY 2017; 38:155-163. [PMID: 28622659 PMCID: PMC5561662 DOI: 10.1016/j.pbi.2017.04.018] [Citation(s) in RCA: 286] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/25/2017] [Indexed: 05/18/2023]
Abstract
After a century of incremental research, technological advances, coupled with a need for sustainable crop yield increases, have reinvigorated the study of beneficial plant-microbe interactions with attention focused on how microbiomes alter plant phenotypes. We review recent advances in plant microbiome research, and describe potential applications for increasing crop productivity. The phylogenetic diversity of plant microbiomes is increasingly well characterized, and their functional diversity is becoming more accessible. Large culture collections are available for controlled experimentation, with more to come. Genetic resources are being brought to bear on questions of microbiome function. We expect that microbial amendments of varying complexities will expose rules governing beneficial plant-microbe interactions contributing to plant growth promotion and disease resistance, enabling more sustainable agriculture.
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Affiliation(s)
- Omri M Finkel
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599-3280, USA.
| | - Gabriel Castrillo
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Sur Herrera Paredes
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Isai Salas González
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
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191
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Vorholt JA, Vogel C, Carlström CI, Müller DB. Establishing Causality: Opportunities of Synthetic Communities for Plant Microbiome Research. Cell Host Microbe 2017; 22:142-155. [DOI: 10.1016/j.chom.2017.07.004] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/25/2017] [Accepted: 07/13/2017] [Indexed: 12/14/2022]
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192
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El Kafsi H, Gorochov G, Larsen M. [Not Available]. Biol Aujourdhui 2017; 211:39-49. [PMID: 28682226 DOI: 10.1051/jbio/2017010] [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: 03/18/2017] [Indexed: 06/07/2023]
Abstract
Genetic evolution of multicellular organisms occurred as a response to environmental challenges, in particular competition for nutrients, climatic change, physical and chemical stressors and pathogens. However organism fitness depends on both the efficiency of its defences and its capacities for benefiting from its symbiotic organisms. Indeed microbes not only engender pathogenies, but enable efficient uptake of host non-self biodegradable nutriments. Furthermore, microbes play an important role in the development of host immunity. We shall review here the associations between some specific genes of the host, microbiota and the immune system. Recent genome-wide association studies disclose that symbiosis between host and microbiota results from a stringent genetic co-evolution. On the other hand, a microbe subset isolated from murine and human microbiotes has been identified on the basis of its interaction with both the host genetics and immunity. Remarkably, microbes which have two such connections are taxonomically related. The best performing bacterial genuses in these two perspectives are Bifidobacterium, Lactobacillus and Akkermansia. We conclude that future therapies targeting microbiota within the framework of chronic inflammatory diseases must consider together host immune and genetic characters associated with microbiota homeostasis.
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Affiliation(s)
- Hela El Kafsi
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris UMRS1135), Sorbonne Universités, UPMC Univ Paris 06, INSERM, Paris, France
| | - Guy Gorochov
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris UMRS1135), Sorbonne Universités, UPMC Univ Paris 06, INSERM, Paris, France - Département d'Immunologie, AP-HP, Groupement Hospitalier Pitié - Salpêtrière, Paris, France
| | - Martin Larsen
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris UMRS1135), Sorbonne Universités, UPMC Univ Paris 06, INSERM, Paris, France - Département d'Immunologie, AP-HP, Groupement Hospitalier Pitié - Salpêtrière, Paris, France
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193
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Susi H, Laine AL. Host resistance and pathogen aggressiveness are key determinants of coinfection in the wild. Evolution 2017; 71:2110-2119. [PMID: 28608539 DOI: 10.1111/evo.13290] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 05/23/2017] [Indexed: 12/24/2022]
Abstract
Coinfection, whereby the same host is infected by more than one pathogen strain, may favor faster host exploitation rates as strains compete for the same limited resources. Hence, coinfection is expected to have major consequences for pathogen evolution, virulence, and epidemiology. Theory predicts genetic variation in host resistance and pathogen infectivity to play a key role in how coinfections are formed. The limited number of studies available has demonstrated coinfection to be a common phenomenon, but little is known about how coinfection varies in space, and what its determinants are. Our aim is to understand how variation in host resistance and pathogen infectivity and aggressiveness contribute to how coinfections are formed in the interaction between fungal pathogen Podosphaera plantaginis and Plantago lanceolata. Our phenotyping study reveals that more aggressive strains are more likely to form coinfections than less aggressive strains in the natural populations. In the natural populations most of the variation in coinfection is found at the individual plant level, and results from a common garden study confirm the prevalence of coinfection to vary significantly among host genotypes. These results show that genetic variation in both the host and pathogen populations are key determinants of coinfection in the wild.
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Affiliation(s)
- Hanna Susi
- Metapopulation Research Centre, Department of Biosciences, PO Box 65 (Viikinkaari 1),, FI-00014, Finland
| | - Anna-Liisa Laine
- Metapopulation Research Centre, Department of Biosciences, PO Box 65 (Viikinkaari 1),, FI-00014, Finland
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194
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Velásquez AC, Oney M, Huot B, Xu S, He SY. Diverse mechanisms of resistance to Pseudomonas syringae in a thousand natural accessions of Arabidopsis thaliana. THE NEW PHYTOLOGIST 2017; 214:1673-1687. [PMID: 28295393 PMCID: PMC5423860 DOI: 10.1111/nph.14517] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 02/07/2017] [Indexed: 05/03/2023]
Abstract
Plants are continuously threatened by pathogen attack and, as such, they have evolved mechanisms to evade, escape and defend themselves against pathogens. However, it is not known what types of defense mechanisms a plant would already possess to defend against a potential pathogen that has not co-evolved with the plant. We addressed this important question in a comprehensive manner by studying the responses of 1041 accessions of Arabidopsis thaliana to the foliar pathogen Pseudomonas syringae pv. tomato (Pst) DC3000. We characterized the interaction using a variety of established methods, including different inoculation techniques, bacterial mutant strains, and assays for the hypersensitive response, salicylic acid (SA) accumulation and reactive oxygen species production . Fourteen accessions showed resistance to infection by Pst DC3000. Of these, two accessions had a surface-based mechanism of resistance, six showed a hypersensitive-like response while three had elevated SA levels. Interestingly, A. thaliana was discovered to have a recognition system for the effector AvrPto, and HopAM1 was found to modulate Pst DC3000 resistance in two accessions. Our comprehensive study has significant implications for the understanding of natural disease resistance mechanisms at the species level and for the ecology and evolution of plant-pathogen interactions.
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Affiliation(s)
| | - Matthew Oney
- MSU-DOE Plant Research Laboratory, East Lansing, MI 48824, USA
| | - Bethany Huot
- MSU-DOE Plant Research Laboratory, East Lansing, MI 48824, USA
- Cell and Molecular Biology Program, Michigan State University, East Lansing, MI 48824, USA
| | - Shu Xu
- MSU-DOE Plant Research Laboratory, East Lansing, MI 48824, USA
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, P. R. China
| | - Sheng Yang He
- MSU-DOE Plant Research Laboratory, East Lansing, MI 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
- Howard Hughes Medical Institute, Gordon and Betty Moore Foundation, Michigan State University, East Lansing, MI 48824, USA
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195
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Frantzeskakis L, Courville KJ, Plücker L, Kellner R, Kruse J, Brachmann A, Feldbrügge M, Göhre V. The Plant-Dependent Life Cycle of Thecaphora thlaspeos: A Smut Fungus Adapted to Brassicaceae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:271-282. [PMID: 28421861 DOI: 10.1094/mpmi-08-16-0164-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Smut fungi are globally distributed plant pathogens that infect agriculturally important crop plants such as maize or potato. To date, molecular studies on plant responses to smut fungi are challenging due to the genetic complexity of their host plants. Therefore, we set out to investigate the known smut fungus of Brassicaceae hosts, Thecaphora thlaspeos. T. thlaspeos infects different Brassicaceae plant species throughout Europe, including the perennial model plant Arabis alpina. In contrast to characterized smut fungi, mature and dry T. thlaspeos teliospores germinated only in the presence of a plant signal. An infectious filament emerges from the teliospore, which can proliferate as haploid filamentous cultures. Haploid filaments from opposite mating types mate, similar to sporidia of the model smut fungus Ustilago maydis. Consistently, the a and b mating locus genes are conserved. Infectious filaments can penetrate roots and aerial tissues of host plants, causing systemic colonization along the vasculature. Notably, we could show that T. thlaspeos also infects Arabidopsis thaliana. Exploiting the genetic resources of A. thaliana and Arabis alpina will allow us to characterize plant responses to smut infection in a comparative manner and, thereby, characterize factors for endophytic growth as well as smut fungi virulence in dicot plants.
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Affiliation(s)
- Lamprinos Frantzeskakis
- 1 Institute for Microbiology, Cluster of Excellence in Plant Sciences, Heinrich-Heine University, Building 26.12.01, Universitätsstr.1, 40205 Düsseldorf, Germany
| | - Kaitlyn J Courville
- 1 Institute for Microbiology, Cluster of Excellence in Plant Sciences, Heinrich-Heine University, Building 26.12.01, Universitätsstr.1, 40205 Düsseldorf, Germany
| | - Lesley Plücker
- 1 Institute for Microbiology, Cluster of Excellence in Plant Sciences, Heinrich-Heine University, Building 26.12.01, Universitätsstr.1, 40205 Düsseldorf, Germany
| | - Ronny Kellner
- 2 Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Julia Kruse
- 3 Institute of Ecology, Evolution and Diversity, Faculty of Biological Sciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany; and
| | - Andreas Brachmann
- 4 Ludwig-Maximilians-Universität München, Faculty of Biology, Genetics, Großhaderner Straße 2-4, 82152 Planegg-Martinsried, Germany
| | - Michael Feldbrügge
- 1 Institute for Microbiology, Cluster of Excellence in Plant Sciences, Heinrich-Heine University, Building 26.12.01, Universitätsstr.1, 40205 Düsseldorf, Germany
| | - Vera Göhre
- 1 Institute for Microbiology, Cluster of Excellence in Plant Sciences, Heinrich-Heine University, Building 26.12.01, Universitätsstr.1, 40205 Düsseldorf, Germany
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196
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Karasov TL, Chae E, Herman JJ, Bergelson J. Mechanisms to Mitigate the Trade-Off between Growth and Defense. THE PLANT CELL 2017; 29:666-680. [PMID: 28320784 PMCID: PMC5435432 DOI: 10.1105/tpc.16.00931] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/23/2017] [Accepted: 03/16/2017] [Indexed: 05/03/2023]
Abstract
Plants have evolved an array of defenses against pathogens. However, mounting a defense response frequently comes with the cost of a reduction in growth and reproduction, carrying critical implications for natural and agricultural populations. This review focuses on how costs are generated and whether and how they can be mitigated. Most well-characterized growth-defense trade-offs stem from antagonistic crosstalk among hormones rather than an identified metabolic expenditure. A primary way plants mitigate such costs is through restricted expression of resistance; this can be achieved through inducible expression of defense genes or by the concentration of defense to particular times or tissues. Defense pathways can be primed for more effective induction, and primed states can be transmitted to offspring. We examine the resistance (R) genes as a case study of how the toll of defense can be generated and ameliorated. The fine-scale regulation of R genes is critical to alleviate the burden of their expression, and the genomic organization of R genes into coregulatory modules reduces costs. Plants can also recruit protection from other species. Exciting new evidence indicates that a plant's genotype influences the microbiome composition, lending credence to the hypothesis that plants shape their microbiome to enhance defense.
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Affiliation(s)
- Talia L Karasov
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Eunyoung Chae
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Jacob J Herman
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637
| | - Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637
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197
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Busby PE, Soman C, Wagner MR, Friesen ML, Kremer J, Bennett A, Morsy M, Eisen JA, Leach JE, Dangl JL. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biol 2017; 15:e2001793. [PMID: 28350798 PMCID: PMC5370116 DOI: 10.1371/journal.pbio.2001793] [Citation(s) in RCA: 351] [Impact Index Per Article: 50.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Feeding a growing world population amidst climate change requires optimizing the reliability, resource use, and environmental impacts of food production. One way to assist in achieving these goals is to integrate beneficial plant microbiomes-i.e., those enhancing plant growth, nutrient use efficiency, abiotic stress tolerance, and disease resistance-into agricultural production. This integration will require a large-scale effort among academic researchers, industry researchers, and farmers to understand and manage plant-microbiome interactions in the context of modern agricultural systems. Here, we identify priorities for research in this area: (1) develop model host-microbiome systems for crop plants and non-crop plants with associated microbial culture collections and reference genomes, (2) define core microbiomes and metagenomes in these model systems, (3) elucidate the rules of synthetic, functionally programmable microbiome assembly, (4) determine functional mechanisms of plant-microbiome interactions, and (5) characterize and refine plant genotype-by-environment-by-microbiome-by-management interactions. Meeting these goals should accelerate our ability to design and implement effective agricultural microbiome manipulations and management strategies, which, in turn, will pay dividends for both the consumers and producers of the world food supply.
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Affiliation(s)
- Posy E. Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Chinmay Soman
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America
| | - Maggie R. Wagner
- Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Maren L. Friesen
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
- Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan, United States of America
| | - James Kremer
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of America
| | - Alison Bennett
- The James Hutton Institute, Invergowrie, Dundee, Scotland
| | - Mustafa Morsy
- College of Natural Sciences and Mathematics, University of West Alabama, Livingston, Alabama, United States of America
| | - Jonathan A. Eisen
- Genome Center, University of California, Davis, California, United States of America
| | - Jan E. Leach
- Bioagricultural Sciences and Pest Management, Colorado State University, Ft Collins, Colorado, United States of America
| | - Jeffery L. Dangl
- Howard Hughes Medical Institute, Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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198
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Liu H, Carvalhais LC, Schenk PM, Dennis PG. Effects of jasmonic acid signalling on the wheat microbiome differ between body sites. Sci Rep 2017; 7:41766. [PMID: 28134326 PMCID: PMC5278374 DOI: 10.1038/srep41766] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 12/28/2016] [Indexed: 11/28/2022] Open
Abstract
Jasmonic acid (JA) signalling helps plants to defend themselves against necrotrophic pathogens and herbivorous insects and has been shown to influence the root microbiome of Arabidopsis thaliana. In this study, we determined whether JA signalling influences the diversity and functioning of the wheat (Triticum aestivum) microbiome and whether these effects are specific to particular parts of the plant. Activation of the JA pathway was achieved via exogenous application of methyl jasmonate and was confirmed by significant increases in the abundance of 10 JA-signalling-related gene transcripts. Phylogenetic marker gene sequencing revealed that JA signalling reduced the diversity and changed the composition of root endophytic but not shoot endophytic or rhizosphere bacterial communities. The total enzymatic activity and substrate utilisation profiles of rhizosphere bacterial communities were not affected by JA signalling. Our findings indicate that the effects of JA signalling on the wheat microbiome are specific to individual plant compartments.
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Affiliation(s)
- Hongwei Liu
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Lilia C Carvalhais
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Peer M Schenk
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Paul G Dennis
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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199
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Bartoli C, Roux F. Genome-Wide Association Studies In Plant Pathosystems: Toward an Ecological Genomics Approach. FRONTIERS IN PLANT SCIENCE 2017; 8:763. [PMID: 28588588 PMCID: PMC5441063 DOI: 10.3389/fpls.2017.00763] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/24/2017] [Indexed: 05/18/2023]
Abstract
The emergence and re-emergence of plant pathogenic microorganisms are processes that imply perturbations in both host and pathogen ecological niches. Global change is largely assumed to drive the emergence of new etiological agents by altering the equilibrium of the ecological habitats which in turn places hosts more in contact with pathogen reservoirs. In this context, the number of epidemics is expected to increase dramatically in the next coming decades both in wild and crop plants. Under these considerations, the identification of the genetic variants underlying natural variation of resistance is a pre-requisite to estimate the adaptive potential of wild plant populations and to develop new breeding resistant cultivars. On the other hand, the prediction of pathogen's genetic determinants underlying disease emergence can help to identify plant resistance alleles. In the genomic era, whole genome sequencing combined with the development of statistical methods led to the emergence of Genome Wide Association (GWA) mapping, a powerful tool for detecting genomic regions associated with natural variation of disease resistance in both wild and cultivated plants. However, GWA mapping has been less employed for the detection of genetic variants associated with pathogenicity in microbes. Here, we reviewed GWA studies performed either in plants or in pathogenic microorganisms (bacteria, fungi and oomycetes). In addition, we highlighted the benefits and caveats of the emerging joint GWA mapping approach that allows for the simultaneous identification of genes interacting between genomes of both partners. Finally, based on co-evolutionary processes in wild populations, we highlighted a phenotyping-free joint GWA mapping approach as a promising tool for describing the molecular landscape underlying plant - microbe interactions.
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200
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Müller DB, Vogel C, Bai Y, Vorholt JA. The Plant Microbiota: Systems-Level Insights and Perspectives. Annu Rev Genet 2016; 50:211-234. [DOI: 10.1146/annurev-genet-120215-034952] [Citation(s) in RCA: 408] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniel B. Müller
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland;
| | - Christine Vogel
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland;
| | - Yang Bai
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Julia A. Vorholt
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland;
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