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Benidire L, El Khalloufi F, Oufdou K, Barakat M, Tulumello J, Ortet P, Heulin T, Achouak W. Phytobeneficial bacteria improve saline stress tolerance in Vicia faba and modulate microbial interaction network. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 729:139020. [PMID: 32498175 DOI: 10.1016/j.scitotenv.2020.139020] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/24/2020] [Accepted: 04/24/2020] [Indexed: 05/25/2023]
Abstract
Increased global warming, caused by climate change and human activities, will seriously hinder plant development, such as increasing salt concentrations in soils, which will limit water availability for plants. To ensure optimal plant growth under such changing conditions, microorganisms that improve plant growth and health must be integrated into agricultural practices. In the present work, we examined the fate of Vicia faba microbiota structure and interaction network upon inoculation with plant-nodulating rhizobia (Rhizobium leguminosarum RhOF125) and non-nodulating strains (Paenibacillus mucilaginosus BLA7 and Ensifer meliloti RhOL1) in the presence (or absence) of saline stress. Inoculated strains significantly improved plant tolerance to saline stress, suggesting either a direct or indirect effect on the plant response to such stress. To determine the structure of microbiota associated with V. faba, samples of the root-adhering soil (RAS), and the root tissues (RT) of seedlings inoculated (or not) with equal population size of RhOF125, BLA7 and RhOL1 strains and grown in the presence (or absence) of salt, were used to profile the microbial composition by 16S rRNA gene sequencing. The inoculation did not show a significant impact on the composition of the RT microbiota or RAS microbiota. The saline stress shifted the RAS microbiota composition, which correlated with a decrease in Enterobacteriaceae and an increase in Sphingobacterium, Chryseobacterium, Stenotrophomonas, Agrobacterium and Sinorhizobium. When the microbiota of roots and RAS are considered together, the interaction networks for each treatment are quite different and display different key populations involved in community assembly. These findings indicate that upon seed inoculation, community interaction networks rather than their composition may contribute to helping plants to better tolerate environmental stresses. The way microbial populations interfere with each other can have an impact on their functions and thus on their ability to express the genes required to help plants tolerate stresses.
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Affiliation(s)
- Loubna Benidire
- Aix-Marseille Univ, CEA, CNRS, UMR7265, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France; Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech, Morocco; High School of Technology Laayoune, Ibn Zohr University, Morocco
| | - Fatima El Khalloufi
- Aix-Marseille Univ, CEA, CNRS, UMR7265, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France; Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech, Morocco; Laboratory of Chemistry, Modeling and Environmental Sciences, Polydisciplinary Faculty of Khouribga, Sultan Moulay Slimane University, Beni Mellal, B.P.: 145, 25000, Khouribga, Morocco
| | - Khalid Oufdou
- Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech, Morocco
| | - Mohamed Barakat
- Aix-Marseille Univ, CEA, CNRS, UMR7265, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France
| | - Joris Tulumello
- Aix-Marseille Univ, CEA, CNRS, UMR7265, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France; Biointrant, SAS BioIntrant, 84120 Pertuis, France
| | - Philippe Ortet
- Aix-Marseille Univ, CEA, CNRS, UMR7265, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France
| | - Thierry Heulin
- Aix-Marseille Univ, CEA, CNRS, UMR7265, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France
| | - Wafa Achouak
- Aix-Marseille Univ, CEA, CNRS, UMR7265, LEMiRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 Saint Paul Lez Durance, France.
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Li Y, Jian X, Li Y, Zeng X, Xu L, Khan MU, Lin W. OsPAL2-1 Mediates Allelopathic Interactions Between Rice and Specific Microorganisms in the Rhizosphere Ecosystem. Front Microbiol 2020; 11:1411. [PMID: 32793125 PMCID: PMC7391800 DOI: 10.3389/fmicb.2020.01411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 05/29/2020] [Indexed: 11/13/2022] Open
Abstract
The use of plant allelopathy to control weeds in the field has been generally recognized as a win-win strategy because it is an environmentally friendly and resource-saving method. The mechanism of this natural weed-control method relies on allelochemicals, the rhizosphere microbiome, and their bio-interaction, and exploring the link between allelochemicals and specific microbes helps accelerate the application of allelopathic characteristics in farming. In this study, we used allelopathic rice PI312777 (PI), its genetically modified OsPAL2-1 repression (PR) or overexpression (PO) lines, and non-allelopathic rice Lemont (Le) as donor plants to reveal the bio-interaction between rice allelochemicals and rhizosphere specific microorganisms. The results showed a higher content of phenolic acid exudation from the roots of PI than those of Le, which resulted in a significantly increased population of Myxococcus in the rhizosphere soil. Transgenic PO lines exhibited increasing exudation of phenolic acid, which led to the population of Myxococcus xanthus in the rhizosphere soil of PO to be significantly increased, while PR showed the opposite result in comparison with wild type PI. Exogenous application of phenolic acid induced the growth of M. xanthus, and the expressions of chemotaxis-related genes were up-regulated in M. xanthus. In addition, quercetin was identified in the culture medium; according to the bioassay determination, a quercetin concentration of 0.53 mM inhibited the root length by 60.59%. Our study indicates that OsPAL2-1 is among the efficient genes that regulate rice allelopathy by controlling the synthesis of phenolic acid allelochemicals, and phenolic acid (ferulic acid, FA) induces the chemotactic aggregation of M. xanthus, which promoted the proliferation and aggregation of this microbe. The potential allelochemical, quercetin was generated from the FA-induced M. xanthus cultured medium.
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Affiliation(s)
- Yingzhe Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Xin Jian
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Yue Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Xiaomei Zeng
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Lining Xu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Muhammad Umar Khan
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China.,Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
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53
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Kumar A, Dubey A. Rhizosphere microbiome: Engineering bacterial competitiveness for enhancing crop production. J Adv Res 2020; 24:337-352. [PMID: 32461810 PMCID: PMC7240055 DOI: 10.1016/j.jare.2020.04.014] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/15/2020] [Accepted: 04/25/2020] [Indexed: 12/29/2022] Open
Abstract
Plants in nature are constantly exposed to a variety of abiotic and biotic stresses which limits their growth and production. Enhancing crop yield and production to feed exponentially growing global population in a sustainable manner by reduced chemical fertilization and agrochemicals will be a big challenge. Recently, the targeted application of beneficial plant microbiome and their cocktails to counteract abiotic and biotic stress is gaining momentum and becomes an exciting frontier of research. Advances in next generation sequencing (NGS) platform, gene editing technologies, metagenomics and bioinformatics approaches allows us to unravel the entangled webs of interactions of holobionts and core microbiomes for efficiently deploying the microbiome to increase crops nutrient acquisition and resistance to abiotic and biotic stress. In this review, we focused on shaping rhizosphere microbiome of susceptible host plant from resistant plant which comprises of specific type of microbial community with multiple potential benefits and targeted CRISPR/Cas9 based strategies for the manipulation of susceptibility genes in crop plants for improving plant health. This review is significant in providing first-hand information to improve fundamental understanding of the process which helps in shaping rhizosphere microbiome.
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Affiliation(s)
- Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, M.P., India
| | - Anamika Dubey
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, M.P., India
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54
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Saad MM, Eida AA, Hirt H. Tailoring plant-associated microbial inoculants in agriculture: a roadmap for successful application. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3878-3901. [PMID: 32157287 PMCID: PMC7450670 DOI: 10.1093/jxb/eraa111] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/09/2020] [Indexed: 05/05/2023]
Abstract
Plants are now recognized as metaorganisms which are composed of a host plant associated with a multitude of microbes that provide the host plant with a variety of essential functions to adapt to the local environment. Recent research showed the remarkable importance and range of microbial partners for enhancing the growth and health of plants. However, plant-microbe holobionts are influenced by many different factors, generating complex interactive systems. In this review, we summarize insights from this emerging field, highlighting the factors that contribute to the recruitment, selection, enrichment, and dynamic interactions of plant-associated microbiota. We then propose a roadmap for synthetic community application with the aim of establishing sustainable agricultural systems that use microbial communities to enhance the productivity and health of plants independently of chemical fertilizers and pesticides. Considering global warming and climate change, we suggest that desert plants can serve as a suitable pool of potentially beneficial microbes to maintain plant growth under abiotic stress conditions. Finally, we propose a framework for advancing the application of microbial inoculants in agriculture.
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Affiliation(s)
- Maged M Saad
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdul Aziz Eida
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Heribert Hirt
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette Cedex, France
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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55
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Fitzpatrick CR, Salas-González I, Conway JM, Finkel OM, Gilbert S, Russ D, Teixeira PJPL, Dangl JL. The Plant Microbiome: From Ecology to Reductionism and Beyond. Annu Rev Microbiol 2020; 74:81-100. [PMID: 32530732 DOI: 10.1146/annurev-micro-022620-014327] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Methodological advances over the past two decades have propelled plant microbiome research, allowing the field to comprehensively test ideas proposed over a century ago and generate many new hypotheses. Studying the distribution of microbial taxa and genes across plant habitats has revealed the importance of various ecological and evolutionary forces shaping plant microbiota. In particular, selection imposed by plant habitats strongly shapes the diversity and composition of microbiota and leads to microbial adaptation associated with navigating the plant immune system and utilizing plant-derived resources. Reductionist approaches have demonstrated that the interaction between plant immunity and the plant microbiome is, in fact, bidirectional and that plants, microbiota, and the environment shape a complex chemical dialogue that collectively orchestrates the plantmicrobiome. The next stage in plant microbiome research will require the integration of ecological and reductionist approaches to establish a general understanding of the assembly and function in both natural and managed environments.
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Affiliation(s)
- Connor R Fitzpatrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; .,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Jonathan M Conway
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Omri M Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Sarah Gilbert
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Dor Russ
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
| | - Paulo José Pereira Lima Teixeira
- Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo (USP), Piracicaba, São Paulo 13418-900, Brazil
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; .,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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56
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Ntalli N, Adamski Z, Doula M, Monokrousos N. Nematicidal Amendments and Soil Remediation. PLANTS (BASEL, SWITZERLAND) 2020; 9:E429. [PMID: 32244565 PMCID: PMC7238745 DOI: 10.3390/plants9040429] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 03/03/2020] [Accepted: 03/21/2020] [Indexed: 12/20/2022]
Abstract
The intensification of agriculture has created concerns about soil degradation and toxicity of agricultural chemicals to non-target organisms. As a result, there is great urgency for discovering new ecofriendly tools for pest management and plant nutrition. Botanical matrices and their extracts and purified secondary metabolites have received much research interest, but time-consuming registration issues have slowed their adoption. In contrast, cultural practices such as use of plant matrices as soil amendments could be immediately used as plant protectants or organic fertilizers. Herein, we focus on some types of soil amendments of botanical origin and their utilization for nematicidal activity and enhancement of plant nutrition. The mode of action is discussed in terms of parasite control as well as plant growth stimulation.
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Affiliation(s)
- Nikoletta Ntalli
- Department of Pesticides Control and Phytopharmacy, Benaki Phytopathological Institute, 8 S. Delta Str., 14561 Athens, Greece
| | - Zbigniew Adamski
- Electron and Confocal Microscope Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614 Poznań, Poland;
- Department of Animal Physiology and Development, Faculty of Biology, Adam Mickiewicz University in Poznań, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Maria Doula
- Laboratory of Non-Parasitic Diseases, Benaki Phytopathological Institute, 8 S. Delta Str., 14561 Athens, Greece;
| | - Nikolaos Monokrousos
- Laboratory of Molecular Ecology, International Hellenic University, 57001 Thessaloniki, Greece;
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57
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Wang CN, Wu RL, Li YY, Qin YF, Li YL, Meng FQ, Wang LG, Xu FL. Effects of pesticide residues on bacterial community diversity and structure in typical greenhouse soils with increasing cultivation years in Northern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 710:136321. [PMID: 31923679 DOI: 10.1016/j.scitotenv.2019.136321] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/18/2019] [Accepted: 12/22/2019] [Indexed: 06/10/2023]
Abstract
The understanding of soil microbiome is important for sustainable cultivation, especially under greenhouse conditions. Here, we investigated the changes in soil pesticide residues and microbial diversity and community structure at different cultivation years under a greenhouse system. The 9-to-14 years sites were found to have the least diversity/rich microbial population as compared to sites under 8 years and over 16 years, as analyzed with alpha diversity index. In total, 42 bacterial phyla were identified across soils with different pesticide residues and cultivation ages. Proteobacteria, Acidobacteria, and Bacteroidetes represented the dominant phyla, that accounted for 34.2-43.4%, 9.7-19.3% and 9.2-16.5% of the total population, respectively. Our data prove that certain pesticides contribute to variation in soil microbial community and that soil bacteria respond differently to cultivation years under greenhouse conditions. Thus, this study provides an insight into microbial community structure changes by pesticides under greenhouse systems and natural biodegradation may have an important part in pesticides soil decontamination.
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Affiliation(s)
- Chao-Nan Wang
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Rui-Lin Wu
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yu-Yan Li
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yi-Fan Qin
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yi-Long Li
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Fan-Qiao Meng
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Li-Gang Wang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Key Laboratory of Agricultural Non-point Source Pollution Control, Ministry of Agriculture, Beijing 100081, China
| | - Fu-Liu Xu
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China.
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58
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Wagner MR, Busby PE, Balint-Kurti P. Analysis of leaf microbiome composition of near-isogenic maize lines differing in broad-spectrum disease resistance. THE NEW PHYTOLOGIST 2020; 225:2152-2165. [PMID: 31657460 DOI: 10.1111/nph.16284] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
Plant genotype strongly affects disease resistance, and also influences the composition of the leaf microbiome. However, these processes have not been studied and linked in the microevolutionary context of breeding for improved disease resistance. We hypothesised that broad-spectrum disease resistance alleles also affect colonisation by nonpathogenic symbionts. Quantitative trait loci (QTL) conferring resistance to multiple fungal pathogens were introgressed into a disease-susceptible maize inbred line. Bacterial and fungal leaf microbiomes of the resulting near-isogenic lines were compared with the microbiome of the disease-susceptible parent line at two time points in multiple fields. Introgression of QTL from disease-resistant lines strongly shifted the relative abundance of diverse fungal and bacterial taxa in both 3-wk-old and 7-wk-old plants. Nevertheless, the effects on overall community structure and diversity were minor and varied among fields and years. Contrary to our expectations, host genotype effects were not any stronger in fields with high disease pressure than in uninfected fields, and microbiome succession over time was similar in heavily infected and uninfected plants. These results show that introgressed QTL can greatly improve broad-spectrum disease resistance while having only limited and inconsistent pleiotropic effects on the leaf microbiome in maize.
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Affiliation(s)
- Maggie R Wagner
- Department of Ecology and Evolutionary Biology, Kansas Biological Survey, University of Kansas, Lawrence, KS, 66047, USA
| | - Posy E Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Peter Balint-Kurti
- Plant Science Research Unit, Agricultural Research Service, United States Department of Agriculture, Raleigh, NC, 27695, USA
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
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59
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Humphrey PT, Whiteman NK. Insect herbivory reshapes a native leaf microbiome. Nat Ecol Evol 2020; 4:221-229. [PMID: 31988447 DOI: 10.1038/s41559-019-1085-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 12/12/2019] [Indexed: 12/22/2022]
Abstract
Insect herbivory is pervasive in plant communities, but its impact on microbial plant colonizers is not well-studied in natural systems. By calibrating sequencing-based bacterial detection to absolute bacterial load, we find that the within-host abundance of most leaf microbiome (phyllosphere) taxa colonizing a native forb is amplified within leaves affected by insect herbivory. Herbivore-associated bacterial amplification reflects community-wide compositional shifts towards lower ecological diversity, but the extent and direction of such compositional shifts can be interpreted only by quantifying absolute abundance. Experimentally eliciting anti-herbivore defences reshaped within-host fitness ranks among Pseudomonas spp. field isolates and amplified a subset of putatively phytopathogenic P. syringae in a manner causally consistent with observed field-scale patterns. Herbivore damage was inversely correlated with plant reproductive success and was highly clustered across plants, which predicts tight co-clustering with putative phytopathogens across hosts. Insect herbivory may thus drive the epidemiology of plant-infecting bacteria as well as the structure of a native plant microbiome by generating variation in within-host bacterial fitness at multiple phylogenetic and spatial scales. This study emphasizes that 'non-focal' biotic interactions between hosts and other organisms in their ecological settings can be crucial drivers of the population and community dynamics of host-associated microbiomes.
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Affiliation(s)
- Parris T Humphrey
- Organismic & Evolutionary Biology, Harvard University, Cambridge, MA, USA. .,Rocky Mountain Biological Laboratory, Crested Butte, CO, USA. .,Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
| | - Noah K Whiteman
- Rocky Mountain Biological Laboratory, Crested Butte, CO, USA.,Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, USA.,Integrative Biology, University of California, Berkeley, CA, USA
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60
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Dundore-Arias JP, Castle SC, Felice L, Dill-Macky R, Kinkel LL. Carbon Amendments Influence Composition and Functional Capacities of Indigenous Soil Microbiomes. Front Mol Biosci 2020; 6:151. [PMID: 31993439 PMCID: PMC6964746 DOI: 10.3389/fmolb.2019.00151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 12/10/2019] [Indexed: 02/01/2023] Open
Abstract
Soil nutrient amendments are recognized for their potential to improve microbial activity and biomass in the soil. However, the specific selective impacts of carbon amendments on indigenous microbiomes and their metabolic functions in agricultural soils remain poorly understood. We investigated the changes in soil chemical characteristics and phenotypes of Streptomyces communities following carbon amendments to soil. Mesocosms were established with soil from two field sites varying in soil organic matter content (low organic matter, LOM; high organic matter, HOM), that were amended at intervals over nine months with low or high dose solutions of glucose, fructose, malic acid, a mixture of these compounds, or water only (non-amended control). Significant shifts in soil chemical characteristics and antibiotic inhibitory capacities of indigenous Streptomyces were observed in response to carbon additions. All high dose carbon amendments consistently increased soil total carbon, while amendments with malic acid decreased soil pH. In LOM soils, higher frequencies of Streptomyces inhibitory phenotypes of the two plant pathogens, Streptomyces scabies and Fusarium oxysporum, were observed in response to soil carbon additions. Additionally, to determine if shifts in Streptomyces functional characteristics correlated with microbiome composition, we investigated whether shifts in functional characteristics of soil Streptomyces correlated with composition of soil bacterial communities, analyzed using 16S rRNA gene sequencing. Regardless of dose, community composition differed significantly among carbon-amended and non-amended soils from both sites. Carbon type and dose had significant effects on bacterial community composition in both LOM and HOM soils. Relationships among microbial community richness (observed species number), diversity, and soil characteristics varied among soils from different sites. These results suggest that manipulation of soil resource availability has the potential to selectively modify the functional capacities of soil microbiomes, and specifically to enhance pathogen inhibitory populations of high value to agricultural systems.
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Affiliation(s)
- José Pablo Dundore-Arias
- Department of Biology and Chemistry, California State University, Monterey Bay, Seaside, CA, United States.,Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Sarah C Castle
- Plant Science Research Unit, USDA-ARS, Saint Paul, MN, United States
| | - Laura Felice
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Linda L Kinkel
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
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61
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Ryu MH, Zhang J, Toth T, Khokhani D, Geddes BA, Mus F, Garcia-Costas A, Peters JW, Poole PS, Ané JM, Voigt CA. Control of nitrogen fixation in bacteria that associate with cereals. Nat Microbiol 2019; 5:314-330. [DOI: 10.1038/s41564-019-0631-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 11/04/2019] [Indexed: 12/23/2022]
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62
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Wang X, Hsu C, Dubeux JCB, Mackowiak C, Blount A, Han X, Liao H. Effects of rhizoma peanut cultivars ( Arachis glabrata Benth.) on the soil bacterial diversity and predicted function in nitrogen fixation. Ecol Evol 2019; 9:12676-12687. [PMID: 31788206 PMCID: PMC6875664 DOI: 10.1002/ece3.5735] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/25/2022] Open
Abstract
There is a growing awareness of the importance of soil microorganisms in agricultural management practices. Currently, much less is known about whether different crop cultivar has an effect on the taxonomic structure and diversity, and specific functions of soil bacterial communities. Here, we examined the changes of the diversity and composition and enzyme-encoding nitrogenase genes in a long-term field experiment with seven different rhizoma peanut cultivars in southeastern USA, coupling high-throughput 16S rRNA gene sequencing and the sequence-based function prediction with Tax4Fun. Of the 32 phyla detected (Proteobacteria class), 13 were dominant: Acidobacteria, Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria, Deltaproteobacteria, Gemmatimonadetes, Firmicutes, Nitrospirae, Chloroflexi, and Planctomycetes (relative abundance >1%). We found no evidence that the diversity and composition of bacterial communities were significantly different among different cultivars, but the abundance of some dominant bacterial groups that have N-fixation potentials (at broad or fine taxonomic level) and predicted abundances of some enzyme-encoding nitrogenase genes showed significant across-cultivar differences. The nitrogenase genes were notably abundant in Florigraze and Latitude soils while remarkably lower in Arbook and UF_TITO soils when compared with other cultivars, indicating different nitrogen fixation potentials among different cultivars. The findings also suggest that the abundance of certain bacterial taxa and the specific function bacteria perform in ecosystems can have an inherent association. Our study is helpful to understand how microbiological responses and feedback to different plant genotypes through the variation in structure and function of their communities in the rhizosphere.
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Affiliation(s)
- Xiao‐Bo Wang
- North Florida Research and Education CenterUniversity of FloridaQuincyFLUSA
- Erguna Forest‐Steppe Ecotone Research StationInstitute of Applied EcologyChinese Academy of SciencesShenyangChina
- Key Laboratory of Vegetation EcologyMinistry of EducationNortheast Normal UniversityChangchunChina
| | - Chih‐Ming Hsu
- North Florida Research and Education CenterUniversity of FloridaQuincyFLUSA
| | - José C. B. Dubeux
- North Florida Research and Education CenterUniversity of FloridaMariannaFLUSA
| | - Cheryl Mackowiak
- North Florida Research and Education CenterUniversity of FloridaQuincyFLUSA
| | - Ann Blount
- North Florida Research and Education CenterUniversity of FloridaMariannaFLUSA
| | - Xing‐Guo Han
- Erguna Forest‐Steppe Ecotone Research StationInstitute of Applied EcologyChinese Academy of SciencesShenyangChina
- Institute of BotanyChinese Academy of SciencesBeijingChina
| | - Hui‐Ling Liao
- North Florida Research and Education CenterUniversity of FloridaQuincyFLUSA
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Shi S, Chang J, Tian L, Nasir F, Ji L, Li X, Tian C. Comparative analysis of the rhizomicrobiome of the wild versus cultivated crop: insights from rice and soybean. Arch Microbiol 2019; 201:879-888. [PMID: 30963196 DOI: 10.1007/s00203-019-01638-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/11/2019] [Accepted: 02/18/2019] [Indexed: 12/30/2022]
Abstract
Plant domestication was a pivotal accomplishment in human history, which led to a reduction in genetic diversity of crop species; however, there was less research focus on how this reduced genetic diversity of crops in affecting rhizosphere microbial communities during crop domestication process. Here, we used high-throughput sequencing to explore the different effects of crops domestication on rhizosphere microbial community structure of rice (Oryza sativa L. and Oryza rufipogon Griff.) and soybean (Glycine max L. and Glycine soja Sieb. et Zucc.). Results indicated that rhizosphere fungal communities are more strongly influenced by crop domestication than bacterial communities. There was a stronger relationship for fungi and bacteria in the cultivated crops than in the wild relatives. Results also showed that the wild varieties had a higher abundance of beneficial symbionts and a lower abundance of pathogens comparing with the cultivated varieties. There was a similar tendency for both rice and soybean in rhizosphere microbial communities by comparing wild crops and their cultivated varieties. In conclusion, crop domestication had a stronger effect on the fungal communities than on the bacterial communities and had improved the microbial relationship in rhizosphere of cultivated crops.
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Affiliation(s)
- Shaohua Shi
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China
| | - Jingjing Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China
| | - Fahad Nasir
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China
| | - Li Ji
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China
| | - Xiujun Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China.
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64
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Darlison J, Mogren L, Rosberg AK, Grudén M, Minet A, Liné C, Mieli M, Bengtsson T, Håkansson Å, Uhlig E, Becher PG, Karlsson M, Alsanius BW. Leaf mineral content govern microbial community structure in the phyllosphere of spinach (Spinacia oleracea) and rocket (Diplotaxis tenuifolia). THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 675:501-512. [PMID: 31030156 DOI: 10.1016/j.scitotenv.2019.04.254] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 06/09/2023]
Abstract
The plant microbiome is an important factor for plant health and productivity. While the impact of nitrogen (N) availability for plant growth and development is well established, its influence on the microbial phyllosphere community structure is unknown. We hypothesize that nitrogen impacts the growth and abundance of several microorganisms on the leaf surface. The bacterial and fungal communities of baby leaf spinach (Spinacia oleracea), and rocket (Diplotaxis tenuifolia) were investigated in a field trial for two years in a commercial setting. Nitrogen fertilizer was tested in four doses (basic nitrogen, basic + suboptimal, basic + commercial, basic + excess) with six replicates in each. Culture-independent (Illumina sequencing) and culture-dependent (viable count and identification of bacterial isolates) community studies were combined with monitoring of plant physiology and site weather conditions. This study found that alpha diversity of bacterial communities decreased in response to increasing nitrogen fertilizer dose, whereas viable counts showed no differences. Correspondingly, fungal communities of the spinach phyllosphere showed a decreasing pattern, whereas the decreasing diversity of fungal communities of rocket was not significant. Plant species and effects of annual variations on microbiome structure were observed for bacterial and fungal communities on both spinach and rocket. This study provides novel insights on the impact of nitrogen fertilizer regime on a nutrient scarce habitat, the phyllosphere.
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Affiliation(s)
- Julia Darlison
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden.
| | - Lars Mogren
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Anna Karin Rosberg
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Maria Grudén
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Antoine Minet
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Clarisse Liné
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Morgane Mieli
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Torbjörn Bengtsson
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Åsa Håkansson
- LTH Lund University, Department of Food Technology, Box 124, SE-221 00 Lund, Sweden
| | - Elisabeth Uhlig
- LTH Lund University, Department of Food Technology, Box 124, SE-221 00 Lund, Sweden
| | - Paul G Becher
- Swedish University of Agricultural Sciences, Department of Plant Protection Biology, PO Box 102, SE-230 53 Alnarp, Sweden
| | - Maria Karlsson
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Beatrix W Alsanius
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
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Newitt JT, Prudence SMM, Hutchings MI, Worsley SF. Biocontrol of Cereal Crop Diseases Using Streptomycetes. Pathogens 2019; 8:pathogens8020078. [PMID: 31200493 PMCID: PMC6630304 DOI: 10.3390/pathogens8020078] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/05/2019] [Accepted: 06/09/2019] [Indexed: 12/12/2022] Open
Abstract
A growing world population and an increasing demand for greater food production requires that crop losses caused by pests and diseases are dramatically reduced. Concurrently, sustainability targets mean that alternatives to chemical pesticides are becoming increasingly desirable. Bacteria in the plant root microbiome can protect their plant host against pests and pathogenic infection. In particular, Streptomyces species are well-known to produce a range of secondary metabolites that can inhibit the growth of phytopathogens. Streptomyces are abundant in soils and are also enriched in the root microbiomes of many different plant species, including those grown as economically and nutritionally valuable cereal crops. In this review we discuss the potential of Streptomyces to protect against some of the most damaging cereal crop diseases, particularly those caused by fungal pathogens. We also explore factors that may improve the efficacy of these strains as biocontrol agents in situ, as well as the possibility of exploiting plant mechanisms, such as root exudation, that enable the recruitment of microbial species from the soil to the root microbiome. We argue that a greater understanding of these mechanisms may enable the development of protective plant root microbiomes with a greater abundance of beneficial bacteria, such as Streptomyces species.
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Affiliation(s)
- Jake T Newitt
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK.
| | - Samuel M M Prudence
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK.
| | - Matthew I Hutchings
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK.
| | - Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK.
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Zhong Y, Yang Y, Liu P, Xu R, Rensing C, Fu X, Liao H. Genotype and rhizobium inoculation modulate the assembly of soybean rhizobacterial communities. PLANT, CELL & ENVIRONMENT 2019; 42:2028-2044. [PMID: 30646427 DOI: 10.1111/pce.13519] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 12/29/2018] [Accepted: 01/07/2019] [Indexed: 06/09/2023]
Abstract
Rhizosphere bacterial communities are vital for plants, yet the composition of rhizobacterial communities and the complex interactions between roots and microbiota, or between microbiota, are largely unknown. In this study, we investigated the structure and composition of rhizobacterial communities in two soybean cultivars and their recombinant inbred lines contrasting in nodulation through 16S rRNA amplicon sequencing in two years of field trials. Our results demonstrate that soybean plants are able to select microbes from bulk soils at the taxonomic and functional level. Soybean genotype significantly influenced the structure of rhizobacterial communities and resulted in dramatically different co-occurrence networks of rhizobacterial communities between different genotypes of soybean plants. Furthermore, the introduction of exogenous rhizobia through inoculation altered soybean rhizobacterial communities in genotype-dependent manner. Rhizobium inoculation not only stimulated the proliferation of potential beneficial microbes but also increased connections in rhizobacterial networks and changed the hub microbes, all of which led to the association of distinctive bacterial communities. Taken together, we demonstrated that the assembly of soybean rhizobacterial communities was determined by both genotype and the introduction of exogenous rhizobia. These findings bolster the feasibility of root microbiome engineering through inoculation of specific microbial constituents.
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Affiliation(s)
- Yongjia Zhong
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yongqing Yang
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Peng Liu
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ruineng Xu
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hong Liao
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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Kudjordjie EN, Sapkota R, Steffensen SK, Fomsgaard IS, Nicolaisen M. Maize synthesized benzoxazinoids affect the host associated microbiome. MICROBIOME 2019; 7:59. [PMID: 30975184 PMCID: PMC6460791 DOI: 10.1186/s40168-019-0677-7] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/28/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Plants actively shape their associated microbial communities by synthesizing bio-active substances. Plant secondary metabolites are known for their signaling and plant defense functions, yet little is known about their overall effect on the plant microbiome. In this work, we studied the effects of benzoxazinoids (BXs), a group of secondary metabolites present in maize, on the host-associated microbial structure. Using BX knock-out mutants and their W22 parental lines, we employed 16S and ITS2 rRNA gene amplicon analysis to characterize the maize microbiome at early growth stages. RESULTS Rhizo-box experiment showed that BXs affected microbial communities not only in roots and shoots, but also in the rhizosphere. Fungal richness in roots was more affected by BXs than root bacterial richness. Maize genotype (BX mutants and their parental lines) as well as plant age explained both fungal and bacterial community structure. Genotypic effect on microbial communities was stronger in roots than in rhizosphere. Diverse, but specific, microbial taxa were affected by BX in both roots and shoots, for instance, many plant pathogens were negatively correlated to BX content. In addition, a co-occurrence analysis of the root microbiome revealed that BXs affected specific groups of the microbiome. CONCLUSIONS This study provides insights into the role of BXs for microbial community assembly in the rhizosphere and in roots and shoots. Coupling the quantification of BX metabolites with bacterial and fungal communities, we were able to suggest a gatekeeper role of BX by showing its correlation with specific microbial taxa and thus providing insights into effects on specific fungal and bacterial taxa in maize roots and shoots. Root microbial co-occurrence networks revealed that BXs affect specific microbial clusters.
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Affiliation(s)
- Enoch Narh Kudjordjie
- Faculty of Science and Technology, Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
| | - Rumakanta Sapkota
- Faculty of Science and Technology, Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
| | - Stine K. Steffensen
- Faculty of Science and Technology, Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
| | - Inge S. Fomsgaard
- Faculty of Science and Technology, Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
| | - Mogens Nicolaisen
- Faculty of Science and Technology, Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
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Singer E, Bonnette J, Kenaley SC, Woyke T, Juenger TE. Plant compartment and genetic variation drive microbiome composition in switchgrass roots. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:185-195. [PMID: 30537406 PMCID: PMC6850097 DOI: 10.1111/1758-2229.12727] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 11/28/2018] [Accepted: 12/04/2018] [Indexed: 05/05/2023]
Abstract
Switchgrass (Panicum virgatum) is a promising biofuel crop native to the United States with genotypes that are adapted to a wide range of distinct ecosystems. Various plants have been shown to undergo symbioses with plant growth-promoting bacteria and fungi, however, plant-associated microbial communities of switchgrass have not been extensively studied to date. We present 16S ribosomal RNA gene and internal transcribed spacer (ITS) data of rhizosphere and root endosphere compartments of four switchgrass genotypes to test the hypothesis that host selection of its root microbiota prevails after transfer to non-native soil. We show that differences in bacterial, archaeal and fungal community composition and diversity are strongly driven by plant compartment and switchgrass genotypes and ecotypes. Plant-associated microbiota show an enrichment in Alphaproteobacteria and Actinobacteria as well as Sordariales and Pleosporales compared with the surrounding soil. Root associated compartments display low-complexity communities dominated and enriched in Actinobacteria, in particular Streptomyces, in the lowland genotypes, and in Alphaproteobacteria, specifically Sphingobium, in the upland genotypes. Our comprehensive root analysis serves as a snapshot of host-specific bacterial and fungal associations of switchgrass in the field and confirms that host-selected microbiomes persist after transfer to non-native soil.
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Affiliation(s)
- Esther Singer
- Department of Energy Joint Genome InstituteWalnut CreekCAUSA
| | - Jason Bonnette
- Department of Integrative Biology, University of Texas AustinAustinTXUSA
| | - Shawn C. Kenaley
- School of Integrative Plant Science, Cornell UniversityIthacaNYUSA
| | - Tanja Woyke
- Department of Energy Joint Genome InstituteWalnut CreekCAUSA
| | - Thomas E. Juenger
- Department of Integrative Biology, University of Texas AustinAustinTXUSA
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69
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Fabiańska I, Gerlach N, Almario J, Bucher M. Plant-mediated effects of soil phosphorus on the root-associated fungal microbiota in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2019; 221:2123-2137. [PMID: 30317641 PMCID: PMC6519159 DOI: 10.1111/nph.15538] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 09/19/2018] [Indexed: 05/22/2023]
Abstract
Plants respond to phosphorus (P) limitation through an array of morphological, physiological and metabolic changes which are part of the phosphate (Pi) starvation response (PSR). This response influences the establishment of the arbuscular mycorrhizal (AM) symbiosis in most land plants. It is, however, unknown to what extent available P and the PSR redefine plant interactions with the fungal microbiota in soil. Using amplicon sequencing of the fungal taxonomic marker ITS2, we examined the changes in root-associated fungal communities in the AM nonhost species Arabidopsis thaliana in response to soil amendment with P and to genetic perturbations in the plant PSR. We observed robust shifts in root-associated fungal communities of P-replete plants in comparison with their P-deprived counterparts, while bulk soil communities remained unaltered. Moreover, plants carrying mutations in the phosphate signaling network genes, phr1, phl1 and pho2, exhibited similarly altered root fungal communities characterized by the depletion of the chytridiomycete taxon Olpidium brassicae specifically under P-replete conditions. This study highlights the nutritional status and the underlying nutrient signaling network of an AM nonhost plant as previously unrecognized factors influencing the assembly of the plant fungal microbiota in response to P in nonsterile soil.
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Affiliation(s)
- Izabela Fabiańska
- Botanical InstituteCologne BiocenterUniversity of CologneCologne50931Germany
| | - Nina Gerlach
- Botanical InstituteCologne BiocenterUniversity of CologneCologne50931Germany
| | - Juliana Almario
- Botanical InstituteCologne BiocenterUniversity of CologneCologne50931Germany
- Cluster of Excellence on Plant Sciences (CEPLAS)University of CologneCologne50931Germany
- Present address:
Center for Plant Molecular BiologyUniversity of TübingenTübingen72074Germany
| | - Marcel Bucher
- Botanical InstituteCologne BiocenterUniversity of CologneCologne50931Germany
- Cluster of Excellence on Plant Sciences (CEPLAS)University of CologneCologne50931Germany
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70
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Achouak W, Abrouk D, Guyonnet J, Barakat M, Ortet P, Simon L, Lerondelle C, Heulin T, Haichar FEZ. Plant hosts control microbial denitrification activity. FEMS Microbiol Ecol 2019; 95:5307930. [DOI: 10.1093/femsec/fiz021] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 02/05/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Wafa Achouak
- Aix Marseille Univ, CEA, CNRS, Laboratory for Microbial Ecology and Extreme Environment (LEMiRE), UMR7265 BVME, F-13108 Saint-Paul-lez-Durance, France
- Aix Marseille Univ, CNRS, FR 3098 ECCOREV, F-13545 Aix-en-Provence, France
| | - Danis Abrouk
- Université de Lyon, Université Lyon1, CNRS, UMR5557, INRA 1418, Ecologie Microbienne, Villeurbanne F-69622, France
| | - Julien Guyonnet
- Université de Lyon, Université Lyon1, CNRS, UMR5557, INRA 1418, Ecologie Microbienne, Villeurbanne F-69622, France
| | - Mohamed Barakat
- Aix Marseille Univ, CEA, CNRS, Laboratory for Microbial Ecology and Extreme Environment (LEMiRE), UMR7265 BVME, F-13108 Saint-Paul-lez-Durance, France
- Aix Marseille Univ, CNRS, FR 3098 ECCOREV, F-13545 Aix-en-Provence, France
| | - Philippe Ortet
- Aix Marseille Univ, CEA, CNRS, Laboratory for Microbial Ecology and Extreme Environment (LEMiRE), UMR7265 BVME, F-13108 Saint-Paul-lez-Durance, France
- Aix Marseille Univ, CNRS, FR 3098 ECCOREV, F-13545 Aix-en-Provence, France
| | - Laurent Simon
- Université de Lyon, Université Lyon 1, UMR5023 LEHNA, CNRS, ENTPE, F‐69622 Villeurbanne Cedex, France
| | - Catherine Lerondelle
- Université de Lyon, Université Lyon1, CNRS, UMR5557, INRA 1418, Ecologie Microbienne, Villeurbanne F-69622, France
| | - Thierry Heulin
- Aix Marseille Univ, CEA, CNRS, Laboratory for Microbial Ecology and Extreme Environment (LEMiRE), UMR7265 BVME, F-13108 Saint-Paul-lez-Durance, France
- Aix Marseille Univ, CNRS, FR 3098 ECCOREV, F-13545 Aix-en-Provence, France
| | - Feth el Zahar Haichar
- Université de Lyon, Université Lyon1, CNRS, UMR5557, INRA 1418, Ecologie Microbienne, Villeurbanne F-69622, France
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Sun G, Du Y, Yin J, Jiang Y, Zhang D, Jiang B, Li G, Wang H, Kong F, Su L, Hu J. Response of microbial communities to different organochlorine pesticides (OCPs) contamination levels in contaminated soils. CHEMOSPHERE 2019; 215:461-469. [PMID: 30336323 DOI: 10.1016/j.chemosphere.2018.09.160] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 09/21/2018] [Accepted: 09/27/2018] [Indexed: 06/08/2023]
Abstract
Understanding microbial community structure and diversity in contaminated soils helps optimize the bioremediation strategies and performance. This study investigated the roles of environmental variables and contamination levels of organochlorine pesticides (OCPs) in shaping microbial community structure at an abandoned aged insecticide plant site. In total, 28 bacterial phyla were identified across soils with different physiochemical properties and OCPs levels. Proteobacteria, Bacterioidetes and Firmicutes represented the dominant lineages, and accounted for 60.2%-69.2%, 5.6%-9.7% and 6.7%-9.4% of the total population, respectively. The overall microbial diversities, in terms of phylogenetic diversity and phylotype richness, were correlated with the contents of hexachlorocyclohexanes (HCHs) and dichlorodiphenyltrichloroethanes (DDTs) in soils, as well as other soil properties including total nitrogen, dissolved organic carbon, pH and vegetation. The multivariate regression tree (MRT) analysis revealed that the soil microbial diversity was significantly impacted by vegetation, which explained 31.8% of the total variation, followed by OCPs level (28.3%), total nitrogen (12.4%), dissolved organic carbon (6.3%) and pH (2.4%). Our findings provide new insights and implications into the impacts on soil microbial community by OCPs contamination and other environmental variables, and offer potential strategic bioremediation for the management of OCPs contaminated sites.
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Affiliation(s)
- Guangdong Sun
- China Institute of Water Resources and Hydropower Research, 100019, China
| | - Yu Du
- School of Environmental Science, Tsinghua University, Beijing, 100084, China; State Key Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, 100084, China.
| | - JunXian Yin
- China Institute of Water Resources and Hydropower Research, 100019, China
| | - YunZhong Jiang
- China Institute of Water Resources and Hydropower Research, 100019, China
| | - Dayi Zhang
- School of Environmental Science, Tsinghua University, Beijing, 100084, China; State Key Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, 100084, China
| | - Bo Jiang
- University of Science and Technology Beijing, 102231, China
| | - Guanghe Li
- School of Environmental Science, Tsinghua University, Beijing, 100084, China; State Key Laboratory of Environmental Simulation and Pollution Control, Tsinghua University, Beijing, 100084, China
| | - Hao Wang
- China Institute of Water Resources and Hydropower Research, 100019, China
| | - Fanxin Kong
- State Key Laboratory of Heavy Oil Processing, Beijing Key Laboratory of Oil & Gas Pollution Control, China; University of Petroleum, Beijing, 102249, China
| | - Limao Su
- China Institute of Water Resources and Hydropower Research, 100019, China
| | - Jialin Hu
- China Institute of Water Resources and Hydropower Research, 100019, China
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Abstract
Stable isotope probing of microbial nucleic acids applied in the rhizosphere enables (a) the identification of the active microbial community involved in root exudate assimilation and those involved in soil organic matter degradation, and (b) the study of the impact of plants via root exudates on the in situ expression of microbial functions. By incubating plants under 13CO2, fresh carbon exuded by the plant will be labeled and hence the microbial community assimilating 13C-root exudates will incorporate 13C into their cellular macromolecules. Labeled DNA, RNA, and proteins can be used to identify microorganisms that assimilated the root exudates. We provide a step-by-step protocol on how to apply stable isotope probing of DNA and RNA in the plant rhizosphere to identify the active microbial communities and analyze their gene expression.
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Pascale A, Proietti S, Pantelides IS, Stringlis IA. Modulation of the Root Microbiome by Plant Molecules: The Basis for Targeted Disease Suppression and Plant Growth Promotion. FRONTIERS IN PLANT SCIENCE 2019; 10:1741. [PMID: 32038698 PMCID: PMC6992662 DOI: 10.3389/fpls.2019.01741] [Citation(s) in RCA: 212] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/11/2019] [Indexed: 05/18/2023]
Abstract
Plants host a mesmerizing diversity of microbes inside and around their roots, known as the microbiome. The microbiome is composed mostly of fungi, bacteria, oomycetes, and archaea that can be either pathogenic or beneficial for plant health and fitness. To grow healthy, plants need to surveil soil niches around the roots for the detection of pathogenic microbes, and in parallel maximize the services of beneficial microbes in nutrients uptake and growth promotion. Plants employ a palette of mechanisms to modulate their microbiome including structural modifications, the exudation of secondary metabolites and the coordinated action of different defence responses. Here, we review the current understanding on the composition and activity of the root microbiome and how different plant molecules can shape the structure of the root-associated microbial communities. Examples are given on interactions that occur in the rhizosphere between plants and soilborne fungi. We also present some well-established examples of microbiome harnessing to highlight how plants can maximize their fitness by selecting their microbiome. Understanding how plants manipulate their microbiome can aid in the design of next-generation microbial inoculants for targeted disease suppression and enhanced plant growth.
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Affiliation(s)
- Alberto Pascale
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Silvia Proietti
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Iakovos S. Pantelides
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
- *Correspondence: Iakovos S. Pantelides, ; Ioannis A. Stringlis,
| | - Ioannis A. Stringlis
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, Netherlands
- *Correspondence: Iakovos S. Pantelides, ; Ioannis A. Stringlis,
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Lombardi N, Vitale S, Turrà D, Reverberi M, Fanelli C, Vinale F, Marra R, Ruocco M, Pascale A, d'Errico G, Woo SL, Lorito M. Root Exudates of Stressed Plants Stimulate and Attract Trichoderma Soil Fungi. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:982-994. [PMID: 29547355 DOI: 10.1094/mpmi-12-17-0310-r] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Plant roots release complex mixtures of bioactive molecules, including compounds that affect the activity and modify the composition of the rhizosphere microbiome. In this work, we investigated the initial phase of the interaction between tomato and an effective biocontrol strain of Trichoderma harzianum (T22). We found that root exudates (RE), obtained from plants grown in a split-root system and exposed to various biotic and abiotic stress factors (wounding, salt, pathogen attack), were able to stimulate the growth and act as chemoattractants of the biocontrol fungus. On the other hand, some of the treatments did not result in an enhanced chemotropism on Fusarium oxysporum f. sp. lycopersici, indicating a mechanism that may be selective for nonpathogenic microbes. The involvement of peroxidases and oxylipins, both known to be released by roots in response to stress, was demonstrated by using RE fractions containing these molecules or their commercial purified analogs, testing the effect of an inhibitor, and characterizing the complex pattern of these metabolites released by tomato roots both locally and systemically.
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Affiliation(s)
- Nadia Lombardi
- 1 Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche
- 2 Dipartimento di Agraria, Università degli Studi di Napoli Federico II, 80055 Portici (NA), Italy
| | - Stefania Vitale
- 3 Departamento de Genetica, Facultad de Ciencias, Campus Rabanales 14071 Córdoba, Spain
| | - David Turrà
- 3 Departamento de Genetica, Facultad de Ciencias, Campus Rabanales 14071 Córdoba, Spain
| | - Massimo Reverberi
- 4 Dipartimento di Biologia Ambientale, Università la Sapienza, 00185 Roma, Italy; and
| | - Corrado Fanelli
- 4 Dipartimento di Biologia Ambientale, Università la Sapienza, 00185 Roma, Italy; and
| | - Francesco Vinale
- 1 Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche
| | - Roberta Marra
- 2 Dipartimento di Agraria, Università degli Studi di Napoli Federico II, 80055 Portici (NA), Italy
| | - Michelina Ruocco
- 1 Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche
| | - Alberto Pascale
- 2 Dipartimento di Agraria, Università degli Studi di Napoli Federico II, 80055 Portici (NA), Italy
| | - Giada d'Errico
- 1 Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche
| | - Sheridan L Woo
- 1 Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche
- 5 Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Matteo Lorito
- 1 Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche
- 2 Dipartimento di Agraria, Università degli Studi di Napoli Federico II, 80055 Portici (NA), Italy
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O’Brien FJM, Dumont MG, Webb JS, Poppy GM. Rhizosphere Bacterial Communities Differ According to Fertilizer Regimes and Cabbage ( Brassica oleracea var. capitata L.) Harvest Time, but Not Aphid Herbivory. Front Microbiol 2018; 9:1620. [PMID: 30083141 PMCID: PMC6064718 DOI: 10.3389/fmicb.2018.01620] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 06/28/2018] [Indexed: 11/16/2022] Open
Abstract
Rhizosphere microbial communities are known to be highly diverse and strongly dependent on various attributes of the host plant, such as species, nutritional status, and growth stage. High-throughput 16S rRNA gene amplicon sequencing has been used to characterize the rhizosphere bacterial community of many important crop species, but this is the first study to date to characterize the bacterial and archaeal community of Brassica oleracea var. capitata. The study also tested the response of the bacterial community to fertilizer type (organic or synthetic) and N dosage (high or low), in addition to plant age (9 or 12 weeks) and aphid (Myzus persicae) herbivory (present/absent). The impact of aboveground herbivory on belowground microbial communities has received little attention in the literature, and since the type (organic or mineral) and amount of fertilizer applications are known to affect M. percicae populations, these treatments were applied at agricultural rates to test for synergistic effects on the soil bacterial community. Fertilizer type and plant growth were found to result in significantly different rhizosphere bacterial communities, while there was no effect of aphid herbivory. Several operational taxonomic units were identified as varying significantly in abundance between the treatment groups and age cohorts. These included members of the S-oxidizing genus Thiobacillus, which was significantly more abundant in organically fertilized 12-week-old cabbages, and the N-fixing cyanobacteria Phormidium, which appeared to decline in synthetically fertilized soils relative to controls. These responses may be an effect of accumulating root-derived glucosinolates in the B. oleracea rhizosphere and increased N-availability, respectively.
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Affiliation(s)
- Flora J. M. O’Brien
- Biological Sciences, University of Southampton, Southampton, United Kingdom
- NIAB EMR, East Malling, United Kingdom
| | - Marc G. Dumont
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Jeremy S. Webb
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Guy M. Poppy
- Biological Sciences, University of Southampton, Southampton, United Kingdom
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76
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Siebers M, Rohr T, Ventura M, Schütz V, Thies S, Kovacic F, Jaeger KE, Berg M, Dörmann P, Schulz M. Disruption of microbial community composition and identification of plant growth promoting microorganisms after exposure of soil to rapeseed-derived glucosinolates. PLoS One 2018; 13:e0200160. [PMID: 29969500 PMCID: PMC6029813 DOI: 10.1371/journal.pone.0200160] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/20/2018] [Indexed: 12/17/2022] Open
Abstract
Land plants are engaged in intricate communities with soil bacteria and fungi indispensable for plant survival and growth. The plant-microbial interactions are largely governed by specific metabolites. We employed a combination of lipid-fingerprinting, enzyme activity assays, high-throughput DNA sequencing and isolation of cultivable microorganisms to uncover the dynamics of the bacterial and fungal community structures in the soil after exposure to isothiocyanates (ITC) obtained from rapeseed glucosinolates. Rapeseed-derived ITCs, including the cyclic, stable goitrin, are secondary metabolites with strong allelopathic affects against other plants, fungi and nematodes, and in addition can represent a health risk for human and animals. However, the effects of ITC application on the different bacterial and fungal organisms in soil are not known in detail. ITCs diminished the diversity of bacteria and fungi. After exposure, only few bacterial taxa of the Gammaproteobacteria, Bacteriodetes and Acidobacteria proliferated while Trichosporon (Zygomycota) dominated the fungal soil community. Many surviving microorganisms in ITC-treated soil where previously shown to harbor plant growth promoting properties. Cultivable fungi and bacteria were isolated from treated soils. A large number of cultivable microbial strains was capable of mobilizing soluble phosphate from insoluble calcium phosphate, and their application to Arabidopsis plants resulted in increased biomass production, thus revealing growth promoting activities. Therefore, inclusion of rapeseed-derived glucosinolates during biofumigation causes losses of microbiota, but also results in enrichment with ITC-tolerant plant microorganisms, a number of which show growth promoting activities, suggesting that Brassicaceae plants can shape soil microbiota community structure favoring bacteria and fungi beneficial for Brassica plants.
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Affiliation(s)
- Meike Siebers
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - Thomas Rohr
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - Marina Ventura
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - Vadim Schütz
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Filip Kovacic
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Martin Berg
- Institute for Organic Agriculture, University of Bonn, Bonn, Germany
- Experimental Farm Wiesengut of University of Bonn, Hennef, Germany
| | - Peter Dörmann
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - Margot Schulz
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
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77
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Wagner MR, Mitchell-Olds T. Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta. Evolution 2018. [PMID: 29522254 DOI: 10.1111/evo.13469] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Phenotypic plasticity is thought to impact evolutionary trajectories by shifting trait values in a direction that is either favored by natural selection ("adaptive" plasticity) or disfavored ("nonadaptive" plasticity). However, it is unclear how commonly each of these types of plasticity occurs in natural populations. To answer this question, we measured glucosinolate defensive chemistry and reproductive fitness in over 1500 individuals of the wild perennial mustard Boechera stricta, planted in four common gardens across central Idaho, United States. Glucosinolate profiles-including total glucosinolate concentration as well as the relative abundances and overall diversity of different compounds-were strongly plastic both among habitats and within habitats. Patterns of glucosinolate plasticity varied greatly among genotypes. Plasticity among sites was predicted to affect fitness in 27.1% of cases; more often than expected by chance, glucosinolate plasticity increased rather than decreased relative fitness. In contrast, we found no evidence for within-habitat selection on glucosinolate reaction norm slopes (i.e., plasticity along a continuous environmental gradient). Together, our results indicate that glucosinolate plasticity may improve the ability of B. stricta populations to persist after migration to new habitats.
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Affiliation(s)
- Maggie R Wagner
- Program in Genetics and Genomics, Department of Biology, Duke University, Durham, North Carolina 27708.,Current Address: Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695
| | - Thomas Mitchell-Olds
- Program in Genetics and Genomics, Department of Biology, Duke University, Durham, North Carolina 27708
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78
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Igiehon NO, Babalola OO. Rhizosphere Microbiome Modulators: Contributions of Nitrogen Fixing Bacteria towards Sustainable Agriculture. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15040574. [PMID: 29570619 PMCID: PMC5923616 DOI: 10.3390/ijerph15040574] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/03/2018] [Accepted: 03/19/2018] [Indexed: 02/05/2023]
Abstract
Rhizosphere microbiome which has been shown to enhance plant growth and yield are modulated or influenced by a few environmental factors such as soil type, plant cultivar, climate change and anthropogenic activities. In particular, anthropogenic activity, such as the use of nitrogen-based chemical fertilizers, is associated with environmental destruction and this calls for a more ecofriendly strategy to increase nitrogen levels in agricultural land. This feat is attainable by harnessing nitrogen-fixing endophytic and free-living rhizobacteria. Rhizobium, Pseudomonas, Azospirillum and Bacillus, have been found to have positive impacts on crops by enhancing both above and belowground biomass and could therefore play positive roles in achieving sustainable agriculture outcomes. Thus, it is necessary to study this rhizosphere microbiome with more sophisticated culture-independent techniques such as next generation sequencing (NGS) with the prospect of discovering novel bacteria with plant growth promoting traits. This review is therefore aimed at discussing factors that can modulate rhizosphere microbiome with focus on the contributions of nitrogen fixing bacteria towards sustainable agricultural development and the techniques that can be used for their study.
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Affiliation(s)
- Nicholas Ozede Igiehon
- Food Security and Safety Niche, Faculty of Natural and Agricultural Science, Private Mail Bag X2046, North West University, Mmabatho 2735, South Africa.
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Science, Private Mail Bag X2046, North West University, Mmabatho 2735, South Africa.
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79
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Ren G, Ma Y, Guo D, Gentry TJ, Hu P, Pierson EA, Gu M. Soil Bacterial Community Was Changed after Brassicaceous Seed Meal Application for Suppression of Fusarium Wilt on Pepper. Front Microbiol 2018; 9:185. [PMID: 29487582 PMCID: PMC5816756 DOI: 10.3389/fmicb.2018.00185] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 01/26/2018] [Indexed: 12/14/2022] Open
Abstract
Application of Brassicaceous seed meal (BSM) is a promising biologically based disease-control practice but BSM could directly and indirectly also affect the non-target bacterial communities, including the beneficial populations. Understanding the bacterial response to BSM at the community level is of great significance for directing plant disease management through the manipulation of resident bacterial communities. Fusarium wilt is a devastating disease on pepper. However, little is known about the response of bacterial communities, especially the rhizosphere bacterial community, to BSM application to soil heavily infested with Fusarium wilt pathogen and cropped with peppers. In this study, a 25-day microcosm incubation of a natural Fusarium wilt pathogen-infested soil supplemented with three BSMs, i.e., Camelina sativa 'Crantz' (CAME), Brassica juncea 'Pacific Gold' (PG), and a mixture of PG and Sinapis alba cv. 'IdaGold' (IG) (PG+IG, 1:1 ratio), was performed. Then, a further 35-day pot experiment was established with pepper plants growing in the BSM treated soils. The changes in the bacterial community in the soil after 25 days of incubation and changes in the rhizosphere after an additional 35 days of pepper growth were investigated by 454 pyrosequencing technique. The results show that the application of PG and PG+IG reduced the disease index by 100% and 72.8%, respectively, after 35 days of pepper growth, while the application of CAME did not have an evident suppressive effect. All BSM treatments altered the bacterial community structure and decreased the bacterial richness and diversity after 25 days of incubation, although this effect was weakened after an additional 35 days of pepper growth. At the phylum/class and the genus levels, the changes in specific bacterial populations resulting from the PG and PG+IG treatments, especially the significant increase in Actinobacteria-affiliated Streptomyces and an unclassified genus and the significant decrease in Chloroflexi, were suspected to be one of the microbial mechanisms involved in PG-containing BSM-induced disease suppression. This study is helpful for our understanding of the mechanisms that lead to contrasting plant disease severity after the addition of different BSMs.
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Affiliation(s)
- Gaidi Ren
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, Nanjing, China
- Key Lab of Food Quality and Safety of Jiangsu Province–State Key Laboratory Breeding Base, Nanjing, China
| | - Yan Ma
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, Nanjing, China
- Key Lab of Food Quality and Safety of Jiangsu Province–State Key Laboratory Breeding Base, Nanjing, China
| | - Dejie Guo
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, Nanjing, China
- Key Lab of Food Quality and Safety of Jiangsu Province–State Key Laboratory Breeding Base, Nanjing, China
| | - Terry J. Gentry
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Ping Hu
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Elizabeth A. Pierson
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - Mengmeng Gu
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
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80
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Wassermann B, Rybakova D, Müller C, Berg G. Harnessing the microbiomes of Brassica vegetables for health issues. Sci Rep 2017; 7:17649. [PMID: 29247170 PMCID: PMC5732279 DOI: 10.1038/s41598-017-17949-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/14/2017] [Indexed: 02/01/2023] Open
Abstract
Plant health is strongly connected with plants´ microbiome. In case of raw-eaten plants, the microbiome can also affect human health. To study potential impacts on health issues of both hosts, the microbiome composition of seven different Brassica vegetables, originating from different food processing pathways, was analyzed by a combined approach of amplicon sequencing, metagenomic mining and cultivation. All Brassica vegetables harbored a highly diverse microbiota as identified by 16S rRNA gene amplicon sequencing. The composition of the microbiota was found to be rather driven by the plant genotype than by the processing pathway. We characterized isolates with potential cancer-preventing properties by tracing myrosinase activity as well as isolates with biological control activity towards plant pathogens. We identified a novel strain with myrosinase activity and we found bacterial myrosinase genes to be enriched in rhizosphere and phyllosphere metagenomes of Brassica napus and Eruca sativa in comparison to the surrounding soil. Strains which were able to suppress plant pathogens were isolated from naturally processed vegetables and represent a substantial part (4.1%) of all vegetable microbiomes. Our results shed first light on the microbiome of edible plants and open the door to harnessing the Brassica microbiome for plant disease resistance and human health.
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Affiliation(s)
- Birgit Wassermann
- Graz University of Technology, Institute of Environmental Biotechnology, Petersgasse 12, 8010, Graz, Austria
| | - Daria Rybakova
- Graz University of Technology, Institute of Environmental Biotechnology, Petersgasse 12, 8010, Graz, Austria
| | - Christina Müller
- Graz University of Technology, Institute of Environmental Biotechnology, Petersgasse 12, 8010, Graz, Austria
| | - Gabriele Berg
- Graz University of Technology, Institute of Environmental Biotechnology, Petersgasse 12, 8010, Graz, Austria.
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81
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Correlated production and consumption of chloromethane in the Arabidopsis thaliana phyllosphere. Sci Rep 2017; 7:17589. [PMID: 29242530 PMCID: PMC5730606 DOI: 10.1038/s41598-017-17421-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/24/2017] [Indexed: 11/24/2022] Open
Abstract
Chloromethane (CH3Cl) is a toxic gas mainly produced naturally, in particular by plants, and its emissions contribute to ozone destruction in the stratosphere. Conversely, CH3Cl can be degraded and used as the sole carbon and energy source by specialised methylotrophic bacteria, isolated from a variety of environments including the phyllosphere, i.e. the aerial parts of vegetation. The potential role of phyllospheric CH3Cl-degrading bacteria as a filter for plant emissions of CH3Cl was investigated using variants of Arabidopsis thaliana with low, wild-type and high expression of HOL1 methyltransferase previously shown to be responsible for most of CH3Cl emissions by A. thaliana. Presence and expression of the bacterial chloromethane dehalogenase cmuA gene in the A. thaliana phyllosphere correlated with HOL1 genotype, as shown by qPCR and RT-qPCR. Production of CH3Cl by A. thaliana paralleled HOL1 expression, as assessed by a fluorescence-based bioreporter. The relation between plant production of CH3Cl and relative abundance of CH3Cl-degrading bacteria in the phyllosphere suggests that CH3Cl-degrading bacteria co-determine the extent of plant emissions of CH3Cl to the atmosphere.
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82
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Gkarmiri K, Mahmood S, Ekblad A, Alström S, Högberg N, Finlay R. Identifying the Active Microbiome Associated with Roots and Rhizosphere Soil of Oilseed Rape. Appl Environ Microbiol 2017; 83:e01938-17. [PMID: 28887416 PMCID: PMC5666129 DOI: 10.1128/aem.01938-17] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 09/06/2017] [Indexed: 12/21/2022] Open
Abstract
RNA stable isotope probing and high-throughput sequencing were used to characterize the active microbiomes of bacteria and fungi colonizing the roots and rhizosphere soil of oilseed rape to identify taxa assimilating plant-derived carbon following 13CO2 labeling. Root- and rhizosphere soil-associated communities of both bacteria and fungi differed from each other, and there were highly significant differences between their DNA- and RNA-based community profiles. Verrucomicrobia, Proteobacteria, Planctomycetes, Acidobacteria, Gemmatimonadetes, Actinobacteria, and Chloroflexi were the most active bacterial phyla in the rhizosphere soil. Bacteroidetes were more active in roots. The most abundant bacterial genera were well represented in both the 13C- and 12C-RNA fractions, while the fungal taxa were more differentiated. Streptomyces, Rhizobium, and Flavobacterium were dominant in roots, whereas Rhodoplanes and Sphingomonas (Kaistobacter) were dominant in rhizosphere soil. "Candidatus Nitrososphaera" was enriched in 13C in rhizosphere soil. Olpidium and Dendryphion were abundant in the 12C-RNA fraction of roots; Clonostachys was abundant in both roots and rhizosphere soil and heavily 13C enriched. Cryptococcus was dominant in rhizosphere soil and less abundant, but was 13C enriched in roots. The patterns of colonization and C acquisition revealed in this study assist in identifying microbial taxa that may be superior competitors for plant-derived carbon in the rhizosphere of Brassica napusIMPORTANCE This microbiome study characterizes the active bacteria and fungi colonizing the roots and rhizosphere soil of Brassica napus using high-throughput sequencing and RNA-stable isotope probing. It identifies taxa assimilating plant-derived carbon following 13CO2 labeling and compares these with other less active groups not incorporating a plant assimilate. Brassica napus is an economically and globally important oilseed crop, cultivated for edible oil, biofuel production, and phytoextraction of heavy metals; however, it is susceptible to several diseases. The identification of the fungal and bacterial species successfully competing for plant-derived carbon, enabling them to colonize the roots and rhizosphere soil of this plant, should enable the identification of microorganisms that can be evaluated in more detailed functional studies and ultimately be used to improve plant health and productivity in sustainable agriculture.
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Affiliation(s)
- Konstantia Gkarmiri
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Shahid Mahmood
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Alf Ekblad
- School of Science and Technology, Örebro University, Örebro, Sweden
| | - Sadhna Alström
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Nils Högberg
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Roger Finlay
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
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83
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Andreote FD, Pereira e Silva MDC. Microbial communities associated with plants: learning from nature to apply it in agriculture. Curr Opin Microbiol 2017; 37:29-34. [DOI: 10.1016/j.mib.2017.03.011] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/22/2017] [Indexed: 01/20/2023]
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84
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van der Meij A, Worsley SF, Hutchings MI, van Wezel GP. Chemical ecology of antibiotic production by actinomycetes. FEMS Microbiol Rev 2017; 41:392-416. [DOI: 10.1093/femsre/fux005] [Citation(s) in RCA: 220] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/02/2017] [Indexed: 12/13/2022] Open
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86
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Lakshmanan V, Ray P, Craven KD. Toward a Resilient, Functional Microbiome: Drought Tolerance-Alleviating Microbes for Sustainable Agriculture. Methods Mol Biol 2017; 1631:69-84. [PMID: 28735391 DOI: 10.1007/978-1-4939-7136-7_4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In recent years, the utilization of novel sequencing techniques opened a new field of research into plant microbiota and was used to explore a wide diversity of microorganisms both inside and outside of plant host tissues, i.e., the endosphere and rhizosphere, respectively. An early realization from such research was that species richness and diversity of the plant microbiome are both greater than believed even a few years ago, and soil is likely home to the most abundant and diverse microbial habitats known. In most ecosystems sampled thus far, overall microbial complexity is determined by the combined influences of plant genotype, soil structure and chemistry, and prevailing environmental conditions, as well as the native "bulk soil" microbial populations from which membership is drawn. Beneficial microorganisms, traditionally referring primarily to nitrogen-fixing bacteria, plant growth-promoting rhizobacteria, and mycorrhizal fungi, play a key role in major functions such as plant nutrition acquisition and plant resistance to biotic and abiotic stresses . Utilization of plant-associated microbes in food production is likely to be critical for twenty-first century agriculture, where arable cropland is limited and food, fiber, and feed productivity must be sustained or even improved with fewer chemical inputs and less irrigation.
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Affiliation(s)
- Venkatachalam Lakshmanan
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Prasun Ray
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Kelly D Craven
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA.
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Shah AN, Iqbal J, Ullah A, Yang G, Yousaf M, Fahad S, Tanveer M, Hassan W, Tung SA, Wang L, Khan A, Wu Y. Allelopathic potential of oil seed crops in production of crops: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:14854-14867. [PMID: 27263104 DOI: 10.1007/s11356-016-6969-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 05/24/2016] [Indexed: 06/05/2023]
Abstract
Agricultural production enhancement has been realized by more consumption of fossil energy such as fertilizer and agrochemicals. However, the production provides the present human with sufficient and diversified commodities, but at the same time, deprives in some extent the resources from the future human as well. In the other hand, it is known that synthetic herbicides face worldwide threats to human's health and environment as well. Therefore, it is a great challenge for agricultural sustainable development. The current review has been focussed on various oilseed crop species which launch efficient allelopathic intervention, either with weeds or other crops. Crop allelopathic properties can make one species more persistent to a native species. Therefore, these crops are potentially harmful to both naturalized as well as agricultural settings. On the other side, allelopathic crops provide strong potential for the development of cultivars that are more highly weed suppressive in managed settings. It is possible to utilize companion plants that have no deleterious effect on neighbor crops and can be included in intercropping system, thus, a mean of contributing to agricultural sustainable development. In mixed culture, replacement method, wherein differing densities of a neighbor species are planted, has been used to study phytotoxic/competitive effects. So, to use alternative ways for weed suppression has become very crucial. Allelochemicals have the ability to create eco-friendly products for weed management, which is beneficial for agricultural sustainable development. Our present study assessed the potential of four oilseed crops for allelopathy on other crops and associated weeds.
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Affiliation(s)
- Adnan Noor Shah
- MOA Key Laboratory of Crop Eco physiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Javaid Iqbal
- Ghazi University, Dera Ghazi Khan, 32200, Punjab, Pakistan
| | - Abid Ullah
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Guozheng Yang
- MOA Key Laboratory of Crop Eco physiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
| | - Muhammad Yousaf
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Shah Fahad
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Mohsin Tanveer
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Waseem Hassan
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Shahbaz Atta Tung
- MOA Key Laboratory of Crop Eco physiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Leishan Wang
- MOA Key Laboratory of Crop Eco physiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Aziz Khan
- MOA Key Laboratory of Crop Eco physiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yingying Wu
- MOA Key Laboratory of Crop Eco physiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
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88
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Wagner MR, Lundberg DS, del Rio TG, Tringe SG, Dangl JL, Mitchell-Olds T. Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nat Commun 2016; 7:12151. [PMID: 27402057 PMCID: PMC4945892 DOI: 10.1038/ncomms12151] [Citation(s) in RCA: 447] [Impact Index Per Article: 55.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 06/06/2016] [Indexed: 01/01/2023] Open
Abstract
Bacteria living on and in leaves and roots influence many aspects of plant health, so the extent of a plant's genetic control over its microbiota is of great interest to crop breeders and evolutionary biologists. Laboratory-based studies, because they poorly simulate true environmental heterogeneity, may misestimate or totally miss the influence of certain host genes on the microbiome. Here we report a large-scale field experiment to disentangle the effects of genotype, environment, age and year of harvest on bacterial communities associated with leaves and roots of Boechera stricta (Brassicaceae), a perennial wild mustard. Host genetic control of the microbiome is evident in leaves but not roots, and varies substantially among sites. Microbiome composition also shifts as plants age. Furthermore, a large proportion of leaf bacterial groups are shared with roots, suggesting inoculation from soil. Our results demonstrate how genotype-by-environment interactions contribute to the complexity of microbiome assembly in natural environments.
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Affiliation(s)
- Maggie R. Wagner
- Program in Genetics and Genomics, Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Derek S Lundberg
- Department of Biology, Curriculum in Genetics and Molecular Biology, Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Tijana G. del Rio
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Susannah G. Tringe
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jeffery L. Dangl
- Department of Biology, Curriculum in Genetics and Molecular Biology, Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Howard Hughes Medical Institute, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Thomas Mitchell-Olds
- Program in Genetics and Genomics, Department of Biology, Duke University, Durham, North Carolina 27708, USA
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Natural variation of root exudates in Arabidopsis thaliana-linking metabolomic and genomic data. Sci Rep 2016; 6:29033. [PMID: 27363486 PMCID: PMC4929559 DOI: 10.1038/srep29033] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 06/14/2016] [Indexed: 12/22/2022] Open
Abstract
Many metabolomics studies focus on aboveground parts of the plant, while metabolism within roots and the chemical composition of the rhizosphere, as influenced by exudation, are not deeply investigated. In this study, we analysed exudate metabolic patterns of Arabidopsis thaliana and their variation in genetically diverse accessions. For this project, we used the 19 parental accessions of the Arabidopsis MAGIC collection. Plants were grown in a hydroponic system, their exudates were harvested before bolting and subjected to UPLC/ESI-QTOF-MS analysis. Metabolite profiles were analysed together with the genome sequence information. Our study uncovered distinct metabolite profiles for root exudates of the 19 accessions. Hierarchical clustering revealed similarities in the exudate metabolite profiles, which were partly reflected by the genetic distances. An association of metabolite absence with nonsense mutations was detected for the biosynthetic pathways of an indolic glucosinolate hydrolysis product, a hydroxycinnamic acid amine and a flavonoid triglycoside. Consequently, a direct link between metabolic phenotype and genotype was detected without using segregating populations. Moreover, genomics can help to identify biosynthetic enzymes in metabolomics experiments. Our study elucidates the chemical composition of the rhizosphere and its natural variation in A. thaliana, which is important for the attraction and shaping of microbial communities.
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90
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Haichar FEZ, Heulin T, Guyonnet JP, Achouak W. Stable isotope probing of carbon flow in the plant holobiont. Curr Opin Biotechnol 2016; 41:9-13. [PMID: 27019410 DOI: 10.1016/j.copbio.2016.02.023] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 01/27/2023]
Abstract
Microbial communities associated with a plant host, constituting a holobiont, affect the physiology and growth of the plant via metabolites that are mainly derived from their photosynthates. The structure and function of active microbial communities that assimilate root exudates can be tracked by using stable isotope probing (SIP) approaches. This article reviews results from ongoing SIP research in plant-microbe interactions, with a specific focus on investigating the fate of fresh and recalcitrant carbon in the rhizosphere with 13C enriched-root exudates, in addition to identifying key players in carbon cycling. Finally, we discuss new SIP applications that have the potential to identify novel enzymes implicated in rhizoremediation or plant genes dedicated to root exudation by combining SIP approaches and genome wide associations studies.
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Affiliation(s)
- Feth El Zahar Haichar
- Université Lyon1, CNRS, UMR5557, INRA, USC1364, Ecologie Microbienne, 69622 Villeurbanne, France.
| | - Thierry Heulin
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA/Cadarache, St-Paul-lez-Durance, France
| | - Julien P Guyonnet
- Université Lyon1, CNRS, UMR5557, INRA, USC1364, Ecologie Microbienne, 69622 Villeurbanne, France
| | - Wafa Achouak
- Laboratory of Microbial Ecology of the Rhizosphere and Extreme Environments (LEMIRE), Aix-Marseille Université, CEA, CNRS, UMR 7265 Biosciences and biotechnology Institute of Aix-Marseille (BIAM), ECCOREV FR 3098, CEA/Cadarache, St-Paul-lez-Durance, France
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91
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Kai M, Effmert U, Piechulla B. Bacterial-Plant-Interactions: Approaches to Unravel the Biological Function of Bacterial Volatiles in the Rhizosphere. Front Microbiol 2016; 7:108. [PMID: 26903987 PMCID: PMC4746483 DOI: 10.3389/fmicb.2016.00108] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/21/2016] [Indexed: 11/13/2022] Open
Abstract
Rhizobacteria produce an enormous amount of volatile compounds, however, the function of these metabolites is scarcely understood. Investigations evaluating influences on plants performed in various laboratories using individually developed experimental setups revealed different and often contradictory results, e.g., ranging from a significant plant growth promotion to a dramatic suppression of plant development. In addition to these discrepancies, these test systems neglected properties and complexity of the rhizosphere. Therefore, to pursue further investigations of the role of bacterial volatiles in this underground habitat, the applied methods have to simulate its natural characteristics as much as possible. In this review, we will describe and discuss pros and cons of currently used bioassays, give insights into rhizosphere characteristics, and suggest improvements for test systems that would consider in natura conditions and would allow gaining further knowledge of the potential function and significance of rhizobacterial volatiles in plant life.
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Affiliation(s)
- Marco Kai
- Department of Biochemistry, Institute of Biological Science, University of Rostock Rostock, Germany
| | - Uta Effmert
- Department of Biochemistry, Institute of Biological Science, University of Rostock Rostock, Germany
| | - Birgit Piechulla
- Department of Biochemistry, Institute of Biological Science, University of Rostock Rostock, Germany
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92
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Tkacz A, Cheema J, Chandra G, Grant A, Poole PS. Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition. THE ISME JOURNAL 2015; 9:2349-59. [PMID: 25909975 PMCID: PMC4611498 DOI: 10.1038/ismej.2015.41] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 02/05/2015] [Accepted: 02/16/2015] [Indexed: 12/15/2022]
Abstract
We examined succession of the rhizosphere microbiota of three model plants (Arabidopsis, Medicago and Brachypodium) in compost and sand and three crops (Brassica, Pisum and Triticum) in compost alone. We used serial inoculation of 24 independent replicate microcosms over three plant generations for each plant/soil combination. Stochastic variation between replicates was surprisingly weak and by the third generation, replicate microcosms for each plant had communities that were very similar to each other but different to those of other plants or unplanted soil. Microbiota diversity remained high in compost, but declined drastically in sand, with bacterial opportunists and putative autotrophs becoming dominant. These dramatic differences indicate that many microbes cannot thrive on plant exudates alone and presumably also require carbon sources and/or nutrients from soil. Arabidopsis had the weakest influence on its microbiota and in compost replicate microcosms converged on three alternative community compositions rather than a single distinctive community. Organisms selected in rhizospheres can have positive or negative effects. Two abundant bacteria are shown to promote plant growth, but in Brassica the pathogen Olpidium brassicae came to dominate the fungal community. So plants exert strong selection on the rhizosphere microbiota but soil composition is critical to its stability. microbial succession/ plant-microbe interactions/rhizosphere microbiota/selection.
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Affiliation(s)
- Andrzej Tkacz
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
- Department of Plant Sciences, Oxford University, Oxford, UK
| | - Jitender Cheema
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Alastair Grant
- Earth and Life Systems Alliance, The School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Philip S Poole
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
- Department of Plant Sciences, Oxford University, Oxford, UK
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93
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Patel JS, Singh A, Singh HB, Sarma BK. Plant genotype, microbial recruitment and nutritional security. FRONTIERS IN PLANT SCIENCE 2015; 6:608. [PMID: 26300905 PMCID: PMC4528164 DOI: 10.3389/fpls.2015.00608] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 07/23/2015] [Indexed: 05/28/2023]
Abstract
Agricultural food products with high nutritional value should always be preferred over food products with low nutritional value. Efforts are being made to increase nutritional value of food by incorporating dietary supplements to the food products. The same is more desirous if the nutritional value of food is increased under natural environmental conditions especially in agricultural farms. Fragmented researches have demonstrated possibilities in achieving the same. The rhizosphere is vital in this regard for not only health and nutritional status of plants but also for the microorganisms colonizing the rhizosphere. Remarkably robust composition of plant microbiome with respect to other soil environments clearly suggests the role of a plant host in discriminating its colonizers (Zancarini et al., 2012). A large number of biotic and abiotic factors are believed to manipulate the microbial communities in the rhizosphere. However, plant genotype has proven to be the key in giving the final shape of the rhizosphere microbiome (Berendsen et al., 2012; Marques et al., 2014).
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Affiliation(s)
- Jai S. Patel
- Department of Botany, Banaras Hindu UniversityVaranasi, India
| | - Akanksha Singh
- Department of Botany, Banaras Hindu UniversityVaranasi, India
| | - Harikesh B. Singh
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu UniversityVaranasi, India
| | - Birinchi K. Sarma
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu UniversityVaranasi, India
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94
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Jørgensen ME, Nour-Eldin HH, Halkier BA. Transport of defense compounds from source to sink: lessons learned from glucosinolates. TRENDS IN PLANT SCIENCE 2015; 20:508-14. [PMID: 25979806 DOI: 10.1016/j.tplants.2015.04.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 04/13/2015] [Accepted: 04/15/2015] [Indexed: 05/20/2023]
Abstract
Plants synthesize a plethora of defense compounds crucial for their survival in a challenging and changing environment. Transport processes are important for shaping the distribution pattern of defense compounds, albeit focus hitherto has been mostly on their biosynthetic pathways. A recent identification of two glucosinolate transporters represents a breakthrough in our understanding of glucosinolate transport in Arabidopsis and has advanced knowledge in transport of defense compounds. In this review, we discuss the role of the glucosinolate transporters in establishing dynamic glucosinolate distribution patterns and source-sink relations. We focus on lessons learned from glucosinolate transport that may apply to transport of other defense compounds and discuss future avenues in the emerging field of defense compound transport.
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Affiliation(s)
- Morten Egevang Jørgensen
- DynaMo, DNRF Center of Excellence, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Hussam Hassan Nour-Eldin
- DynaMo, DNRF Center of Excellence, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Barbara Ann Halkier
- DynaMo, DNRF Center of Excellence, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Frederiksberg C, Denmark.
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95
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Hanschen FS, Yim B, Winkelmann T, Smalla K, Schreiner M. Degradation of Biofumigant Isothiocyanates and Allyl Glucosinolate in Soil and Their Effects on the Microbial Community Composition. PLoS One 2015; 10:e0132931. [PMID: 26186695 PMCID: PMC4505889 DOI: 10.1371/journal.pone.0132931] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 06/20/2015] [Indexed: 01/08/2023] Open
Abstract
Brassicales species rich in glucosinolates are used for biofumigation, a process based on releasing enzymatically toxic isothiocyanates into the soil. These hydrolysis products are volatile and often reactive compounds. Moreover, glucosinolates can be degraded also without the presence of the hydrolytic enzyme myrosinase which might contribute to bioactive effects. Thus, in the present study the stability of Brassicaceae plant-derived and pure glucosinolates hydrolysis products was studied using three different soils (model biofumigation). In addition, the degradation of pure 2-propenyl glucosinolate was investigated with special regard to the formation of volatile breakdown products. Finally, the influence of pure glucosinolate degradation on the bacterial community composition was evaluated using denaturing gradient gel electrophoresis of 16S rRNA gene amplified from total community DNA. The model biofumigation study revealed that the structure of the hydrolysis products had a significant impact on their stability in the soil but not the soil type. Following the degradation of pure 2-propenyl glucosinolate in the soils, the nitrile as well as the isothiocyanate can be the main degradation products, depending on the soil type. Furthermore, the degradation was shown to be both chemically as well as biologically mediated as autoclaving reduced degradation. The nitrile was the major product of the chemical degradation and its formation increased with iron content of the soil. Additionally, the bacterial community composition was significantly affected by adding pure 2-propenyl glucosinolate, the effect being more pronounced than in treatments with myrosinase added to the glucosinolate. Therefore, glucosinolates can have a greater effect on soil bacterial community composition than their hydrolysis products.
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Affiliation(s)
- Franziska S. Hanschen
- Department of Quality, Leibniz-Institute of Vegetable and Ornamental Crops Grossbeeren/Erfurt e.V., Theodor-Echtermeyer-Weg 1, D-14979 Grossbeeren, Germany
| | - Bunlong Yim
- Institute of Horticultural Production Systems, Leibniz Universität Hannover, Section of Woody Plant and Propagation Physiology, Herrenhäuser Str. 2, D-30419 Hannover, Germany
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Messeweg 11–12, D-38104 Braunschweig, Germany
| | - Traud Winkelmann
- Institute of Horticultural Production Systems, Leibniz Universität Hannover, Section of Woody Plant and Propagation Physiology, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Messeweg 11–12, D-38104 Braunschweig, Germany
| | - Monika Schreiner
- Department of Quality, Leibniz-Institute of Vegetable and Ornamental Crops Grossbeeren/Erfurt e.V., Theodor-Echtermeyer-Weg 1, D-14979 Grossbeeren, Germany
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Kerwin R, Feusier J, Corwin J, Rubin M, Lin C, Muok A, Larson B, Li B, Joseph B, Francisco M, Copeland D, Weinig C, Kliebenstein DJ. Natural genetic variation in Arabidopsis thaliana defense metabolism genes modulates field fitness. eLife 2015; 4. [PMID: 25867014 PMCID: PMC4396512 DOI: 10.7554/elife.05604] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 03/18/2015] [Indexed: 01/06/2023] Open
Abstract
Natural populations persist in complex environments, where biotic stressors, such as pathogen and insect communities, fluctuate temporally and spatially. These shifting biotic pressures generate heterogeneous selective forces that can maintain standing natural variation within a species. To directly test if genes containing causal variation for the Arabidopsis thaliana defensive compounds, glucosinolates (GSL) control field fitness and are therefore subject to natural selection, we conducted a multi-year field trial using lines that vary in only specific causal genes. Interestingly, we found that variation in these naturally polymorphic GSL genes affected fitness in each of our environments but the pattern fluctuated such that highly fit genotypes in one trial displayed lower fitness in another and that no GSL genotype or genotypes consistently out-performed the others. This was true both across locations and within the same location across years. These results indicate that environmental heterogeneity may contribute to the maintenance of GSL variation observed within Arabidopsis thaliana. DOI:http://dx.doi.org/10.7554/eLife.05604.001 ‘Genetic variation’ describes the naturally occurring differences in DNA sequences that are found among individuals of the same species. These genetic differences arise from random mutations and may be passed on to their offspring. Some of these mutations may improve the ability of an individual to survive and reproduce—known as fitness—and are likely to become more common in the population. Other mutations may reduce an individual's fitness and are likely to be lost. However, it is believed that most of the mutations will have no effect on the fitness of individuals. It is not known why many of these ‘neutral’ genetic differences are maintained in populations. Some researchers have proposed that they are kept by chance and that there is no direct advantage to the population of keeping them unless these neutral mutations later become beneficial. However, other researchers think that the genetic variation itself may improve the fitness of the population by allowing it to quickly adapt to changes in the environment. Arabidopsis thaliana is a small plant that lives in many different environments and has high levels of genetic variation in many of its physical traits. One of these traits is the production of molecules called glucosinolates, which help the plants to defend against herbivores and infection by microbes. Previous studies have suggested that variation in the genes that make glucosinolates may improve the fitness of A. thaliana populations. To test this idea, Kerwin et al. carried out a field trial using A. thaliana plants that were genetically identical except for some of the genes involved in the production of glucosinolates. Kerwin et al. grew the plants in several different environments over several years. The field trial shows that variation in these genes affected the fitness of the plants in each of the different environments. However, the fitness benefit depended on the environment, and no single gene variant provided the best fitness across all environments, or over all the years of the trial. Kerwin et al.'s findings suggest that changes in the environment may contribute to the maintenance of genetic variation in the genes that make glucosinolates. This raises the questions of how many other genes in plants (or other species such as humans) have genetic variation that contributes to fitness across varied environments; and how can this link be tested in natural settings. DOI:http://dx.doi.org/10.7554/eLife.05604.002
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Affiliation(s)
- Rachel Kerwin
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Julie Feusier
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Jason Corwin
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Matthew Rubin
- Department of Botany, University of Wyoming, Laramie, United States
| | - Catherine Lin
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Alise Muok
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Brandon Larson
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Baohua Li
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Bindu Joseph
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Marta Francisco
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Daniel Copeland
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Cynthia Weinig
- Department of Genetics, University of Utah, Salt Lake City, United States
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Reinhold-Hurek B, Bünger W, Burbano CS, Sabale M, Hurek T. Roots shaping their microbiome: global hotspots for microbial activity. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:403-24. [PMID: 26243728 DOI: 10.1146/annurev-phyto-082712-102342] [Citation(s) in RCA: 303] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Land plants interact with microbes primarily at roots. Despite the importance of root microbial communities for health and nutrient uptake, the current understanding of the complex plant-microbe interactions in the rhizosphere is still in its infancy. Roots provide different microhabitats at the soil-root interface: rhizosphere soil, rhizoplane, and endorhizosphere. We discuss technical aspects of their differentiation that are relevant for the functional analysis of their different microbiomes, and we assess PCR (polymerase chain reaction)-based methods to analyze plant-associated bacterial communities. Development of novel primers will allow a less biased and more quantitative view of these global hotspots of microbial activity. Based on comparison of microbiome data for the different root-soil compartments and on knowledge of bacterial functions, a three-step enrichment model for shifts in community structure from bulk soil toward roots is presented. To unravel how plants shape their microbiome, a major research field is likely to be the coupling of reductionist and molecular ecological approaches, particularly for specific plant genotypes and mutants, to clarify causal relationships in complex root communities.
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Affiliation(s)
- Barbara Reinhold-Hurek
- Department of Microbe-Plant Interactions, Faculty of Biology and Chemistry, University of Bremen, D-28334 Bremen, Germany; , , , ,
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Dufour V, Stahl M, Baysse C. The antibacterial properties of isothiocyanates. MICROBIOLOGY-SGM 2014; 161:229-243. [PMID: 25378563 DOI: 10.1099/mic.0.082362-0] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Isothiocyanates (ITCs) are natural plant products generated by the enzymic hydrolysis of glucosinolates found in Brassicaceae vegetables. These natural sulfur compounds and their dithiocarbamate conjugates have been previously evaluated for their anti-cancerous properties. Their antimicrobial properties have been previously studied as well, mainly for food preservation and plant pathogen control. Recently, several revelations concerning the mode of action of ITCs in prokaryotes have emerged. This review addresses these new studies and proposes a model to summarize the current knowledge and hypotheses for the antibacterial effect of ITCs and whether they may provide the basis for the design of novel antibiotics.
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Affiliation(s)
- Virginie Dufour
- Equipe EA1254, Microbiologie Risques Infectieux, University of Rennes 1, F-35042 Rennes cedex, France
| | - Martin Stahl
- Division of Gastroenterology, BC's Children's Hospital, Child and Family Research Institute and University of British Columbia, Vancouver, BC, Canada
| | - Christine Baysse
- Equipe EA1254, Microbiologie Risques Infectieux, University of Rennes 1, F-35042 Rennes cedex, France
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99
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Tian Y, Gao L. Bacterial diversity in the rhizosphere of cucumbers grown in soils covering a wide range of cucumber cropping histories and environmental conditions. MICROBIAL ECOLOGY 2014; 68:794-806. [PMID: 25027276 DOI: 10.1007/s00248-014-0461-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 07/04/2014] [Indexed: 06/03/2023]
Abstract
Rhizosphere microorganisms in soils are important for plant growth. However, the importance of rhizosphere microorganisms is still underestimated since many microorganisms associated with plant roots cannot be cultured and since the microbial diversity in the rhizosphere can be influenced by several factors, such as the cropping history, biogeography, and agricultural practice. Here, we characterized the rhizosphere bacterial diversity of cucumber plants grown in soils covering a wide range of cucumber cropping histories and environmental conditions by using pyrosequencing of bacterial 16S rRNA genes. We also tested the effects of compost addition and/or bacterial inoculation on the bacterial diversity in the rhizosphere. We identified an average of approximately 8,883 reads per sample, corresponding to around 4,993 molecular operational taxonomic units per sample. The Proteobacteria was the most abundant phylum in almost all soils. The abundances of the phyla Bacteroidetes, Actinobacteria, Firmicutes, Acidobacteria, and Verrucomicrobia varied among the samples, and together with Proteobacteria, these phyla were the six most abundant phyla in almost all analyzed samples. Analyzing all the sample libraries together, the predominant genera found were Flavobacterium, Ohtaekwangia, Opitutus, Gp6, Steroidobacter, and Acidovorax. Overall, compost and microbial amendments increased shoot biomass when compared to untreated soils. However, compost addition decreased the bacterial α-diversity in most soils (but for three soils compost increased diversity), and no statistical effect of microbial amendment on the bacterial α-diversity was found. Moreover, soil amendments did not significantly influence the bacterial β-diversity. Soil organic content appeared more important than compost and microbial amendments in shaping the structure of bacterial communities in the rhizosphere of cucumber.
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Affiliation(s)
- Yongqiang Tian
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Agricultural and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing, 100193, China,
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100
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Lakshmanan V, Selvaraj G, Bais HP. Functional soil microbiome: belowground solutions to an aboveground problem. PLANT PHYSIOLOGY 2014; 166:689-700. [PMID: 25059708 PMCID: PMC4213098 DOI: 10.1104/pp.114.245811] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 07/23/2014] [Indexed: 05/07/2023]
Abstract
There is considerable evidence in the literature that beneficial rhizospheric microbes can alter plant morphology, enhance plant growth, and increase mineral content. Of late, there is a surge to understand the impact of the microbiome on plant health. Recent research shows the utilization of novel sequencing techniques to identify the microbiome in model systems such as Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). However, it is not known how the community of microbes identified may play a role to improve plant health and fitness. There are very few detailed studies with isolated beneficial microbes showing the importance of the functional microbiome in plant fitness and disease protection. Some recent work on the cultivated microbiome in rice (Oryza sativa) shows that a wide diversity of bacterial species is associated with the roots of field-grown rice plants. However, the biological significance and potential effects of the microbiome on the host plants are completely unknown. Work performed with isolated strains showed various genetic pathways that are involved in the recognition of host-specific factors that play roles in beneficial host-microbe interactions. The composition of the microbiome in plants is dynamic and controlled by multiple factors. In the case of the rhizosphere, temperature, pH, and the presence of chemical signals from bacteria, plants, and nematodes all shape the environment and influence which organisms will flourish. This provides a basis for plants and their microbiomes to selectively associate with one another. This Update addresses the importance of the functional microbiome to identify phenotypes that may provide a sustainable and effective strategy to increase crop yield and food security.
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Affiliation(s)
- Venkatachalam Lakshmanan
- Department of Plant and Soil Sciences, University of Delaware, and Delaware Biotechnology Institute, Newark, Delaware 19711
| | - Gopinath Selvaraj
- Department of Plant and Soil Sciences, University of Delaware, and Delaware Biotechnology Institute, Newark, Delaware 19711
| | - Harsh P Bais
- Department of Plant and Soil Sciences, University of Delaware, and Delaware Biotechnology Institute, Newark, Delaware 19711
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