151
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Yang M, Mavrodi DV, Mavrodi OV, Thomashow LS, Weller DM. Exploring the Pathogenicity of Pseudomonas brassicacearum Q8r1-96 and Other Strains of the Pseudomonas fluorescens Complex on Tomato. PLANT DISEASE 2020; 104:1026-1031. [PMID: 31994984 PMCID: PMC7163159 DOI: 10.1094/pdis-09-19-1989-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Pseudomonas brassicacearum and related species of the P. fluorescens complex have long been studied as biocontrol and growth-promoting rhizobacteria involved in suppression of soilborne pathogens. We report here that P. brassicacearum Q8r1-96 and other 2,4-diacetylphloroglucinol (DAPG)-producing fluorescent pseudomonads involved in take-all decline of wheat in the Pacific Northwest of the United States can also be pathogenic to other plant hosts. Strain Q8r1-96 caused necrosis when injected into tomato stems and immature tomato fruits, either attached or removed from the plant, but lesion development was dose dependent, with a minimum of 106 CFU ml-1 required to cause visible tissue damage. We explored the relative contribution of several known plant-microbe interaction traits to the pathogenicity of strain Q8r1-96. Type III secretion system (T3SS) mutants of Q8r1-96, injected at a concentration of 108 CFU ml-1, were significantly less virulent, but not consistently, as compared with the wild-type strain. However, a DAPG-deficient phlD mutant of Q8r1-96 was significantly and consistently less virulent as compared with the wild type. Strain Q8r1-96acc, engineered to over express ACC deaminase, caused a similar amount of necrosis as the wild type. Cell-free culture filtrates of strain Q8r1-96 and pure DAPG also cause necrosis in tomato fruits. Our results suggest that DAPG plays a significant role in the ability of Q8r1-96 to cause necrosis of tomato tissue, but other factors also contribute to the pathogenic properties of this organism.
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Affiliation(s)
- Mingming Yang
- Corresponding authors: Mingming Yang: ; David M. Weller:
| | - Dmitri V. Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Olga V. Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Linda S. Thomashow
- U. S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164-6430, USA
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152
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Pineda A, Kaplan I, Hannula SE, Ghanem W, Bezemer TM. Conditioning the soil microbiome through plant-soil feedbacks suppresses an aboveground insect pest. THE NEW PHYTOLOGIST 2020; 226:595-608. [PMID: 31863484 PMCID: PMC7155073 DOI: 10.1111/nph.16385] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 12/04/2019] [Indexed: 05/21/2023]
Abstract
Soils and their microbiomes are now recognized as key components of plant health, but how to steer those microbiomes to obtain their beneficial functions is still unknown. Here, we assess whether plant-soil feedbacks can be applied in a crop system to shape soil microbiomes that suppress herbivorous insects in above-ground tissues. We used four grass and four forb species to condition living soil. Then we inoculated those soil microbiomes into sterilized soil and grew chrysanthemum as a focal plant. We evaluated the soil microbiome in the inocula and after chrysanthemum growth, as well as plant and herbivore parameters. We show that inocula and inoculated soil in which a focal plant had grown harbor remarkably different microbiomes, with the focal plant exerting a strong negative effect on fungi, especially arbuscular mycorrhizal fungi. Soil inoculation consistently induced resistance against the thrips Frankliniella occidentalis, but not against the mite Tetranychus urticae, when compared with sterilized soil. Additionally, plant species shaped distinct microbiomes that had different effects on thrips, chlorogenic acid concentrations in leaves and plant growth. This study provides a proof-of-concept that the plant-soil feedback concept can be applied to steer soil microbiomes with the goal of inducing resistance above ground against herbivorous insects.
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Affiliation(s)
- Ana Pineda
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)Wageningen6700 ABthe Netherlands
| | - Ian Kaplan
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)Wageningen6700 ABthe Netherlands
- Department of EntomologyPurdue UniversityWest LafayetteIN47907USA
| | - S. Emilia Hannula
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)Wageningen6700 ABthe Netherlands
| | - Wadih Ghanem
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)Wageningen6700 ABthe Netherlands
- Department of EntomologyPurdue UniversityWest LafayetteIN47907USA
| | - T. Martijn Bezemer
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)Wageningen6700 ABthe Netherlands
- Institute of BiologySection Plant Ecology and PhytochemistryLeiden UniversityLeiden2300 RAthe Netherlands
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153
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Edge TA, Baird DJ, Bilodeau G, Gagné N, Greer C, Konkin D, Newton G, Séguin A, Beaudette L, Bilkhu S, Bush A, Chen W, Comte J, Condie J, Crevecoeur S, El-Kayssi N, Emilson EJS, Fancy DL, Kandalaft I, Khan IUH, King I, Kreutzweiser D, Lapen D, Lawrence J, Lowe C, Lung O, Martineau C, Meier M, Ogden N, Paré D, Phillips L, Porter TM, Sachs J, Staley Z, Steeves R, Venier L, Veres T, Watson C, Watson S, Macklin J. The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 710:135906. [PMID: 31926407 DOI: 10.1016/j.scitotenv.2019.135906] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 11/29/2019] [Accepted: 12/01/2019] [Indexed: 06/10/2023]
Abstract
Transformative advances in metagenomics are providing an unprecedented ability to characterize the enormous diversity of microorganisms and invertebrates sustaining soil health and water quality. These advances are enabling a better recognition of the ecological linkages between soil and water, and the biodiversity exchanges between these two reservoirs. They are also providing new perspectives for understanding microorganisms and invertebrates as part of interacting communities (i.e. microbiomes and zoobiomes), and considering plants, animals, and humans as holobionts comprised of their own cells as well as diverse microorganisms and invertebrates often acquired from soil and water. The Government of Canada's Genomics Research and Development Initiative (GRDI) launched the Ecobiomics Project to coordinate metagenomics capacity building across federal departments, and to apply metagenomics to better characterize microbial and invertebrate biodiversity for advancing environmental assessment, monitoring, and remediation activities. The Project has adopted standard methods for soil, water, and invertebrate sampling, collection and provenance of metadata, and nucleic acid extraction. High-throughput sequencing is located at a centralized sequencing facility. A centralized Bioinformatics Platform was established to enable a novel government-wide approach to harmonize metagenomics data collection, storage and bioinformatics analyses. Sixteen research projects were initiated under Soil Microbiome, Aquatic Microbiome, and Invertebrate Zoobiome Themes. Genomic observatories were established at long-term environmental monitoring sites for providing more comprehensive biodiversity reference points to assess environmental change.
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Affiliation(s)
- Thomas A Edge
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Donald J Baird
- Environment and Climate Change Canada @ Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.
| | | | - Nellie Gagné
- Fisheries and Oceans Canada, Moncton, New Brunswick, Canada
| | - Charles Greer
- National Research Council Canada, Montreal, Quebec, Canada
| | - David Konkin
- National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Glen Newton
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | | | - Lee Beaudette
- Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Satpal Bilkhu
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Alexander Bush
- Environment and Climate Change Canada @ Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Wen Chen
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Jérôme Comte
- Environment and Climate Change Canada, Burlington, Ontario, Canada; Institut National de la Recherche Scientifique, Québec, Québec, Canada
| | - Janet Condie
- National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | | | | | - Erik J S Emilson
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada
| | - Donna-Lee Fancy
- National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Iyad Kandalaft
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Izhar U H Khan
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Ian King
- Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - David Kreutzweiser
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada
| | - David Lapen
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - John Lawrence
- Environment and Climate Change Canada, Saskatoon, Saskatchewan, Canada
| | - Christine Lowe
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Oliver Lung
- Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
| | | | - Matthew Meier
- Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Nicholas Ogden
- Public Health Agency of Canada, St. Hyacinthe, Quebec, Canada
| | - David Paré
- Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Lori Phillips
- Agriculture and Agri-Food Canada, Harrow, Ontario, Canada
| | - Teresita M Porter
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada; Biodiversity Institute of Ontario, University of Guelph, Ontario, Canada
| | - Joel Sachs
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Zachery Staley
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Royce Steeves
- Fisheries and Oceans Canada, Moncton, New Brunswick, Canada
| | - Lisa Venier
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada
| | - Teodor Veres
- National Research Council Canada, Ottawa, Ontario, Canada
| | - Cynthia Watson
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Susan Watson
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - James Macklin
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
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154
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Ullah H, Yasmin H, Mumtaz S, Jabeen Z, Naz R, Nosheen A, Hassan MN. Multitrait Pseudomonas spp. Isolated from Monocropped Wheat ( Triticum aestivum) Suppress Fusarium Root and Crown Rot. PHYTOPATHOLOGY 2020; 110:582-592. [PMID: 31799901 DOI: 10.1094/phyto-10-19-0383-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fusarium root and crown rot is the most common disease of wheat, especially wheat grown in arid zones where drought is a common issue. The development of environmentally safe approaches to manage diseases of food crops is important for humans. The monocropping system recruits beneficial bacteria that promote plant growth through nutrient solubilization and pathogen suppression. In this study, a field where wheat was monocropped for 5 successive years under rainfed conditions was identified. A total of 29 bacterial isolates were obtained from the rhizosphere, endosphere, and phyllosphere of wheat at its harvesting stage. The Gram-negative bacteria were less prevalent (41%) but the majority (75%) exhibited plant growth-promoting traits. The ability of strains to solubilize nutrients (solubilization index = 2.3 to 4), inhibit pathogenic fungi (25 to 56%), and produce antifungal compounds was highly variable. The rhizobacteria significantly promoted the growth and disease resistance of wheat varieties such as Pirsbak-2015 and Galaxy-2013 by inducing antioxidant enzyme activity (0.2- to 2.1-fold). The bacterial strains were identified as Ochrobactrum spp., Acinetobacter spp., and Pseudomonas mediterranea by 16S rRNA and rpoD sequence analysis. The endophytic bacterium P. mediterranea HU-9 exhibited maximum biocontrol efficacy against wheat root and crown rot diseases with a disease score/disease index from 1.8 to 3.1. The monocropping systems of rainfed agriculture are an ideal source of beneficial bacteria to use as bioinoculants for different crops.
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Affiliation(s)
- Habib Ullah
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Humaira Yasmin
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Saqib Mumtaz
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Zahra Jabeen
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Rabia Naz
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Asia Nosheen
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
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155
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Friend or foe? Exploring the fine line between Pseudomonas brassicacearum and phytopathogens. J Med Microbiol 2020; 69:347-360. [DOI: 10.1099/jmm.0.001145] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Pseudomonas brassicacearum
is one of over fifty species of bacteria classified into the
P. fluorescens
group. Generally considered a harmless commensal, these bacteria are studied for their plant-growth promotion (PGP) and biocontrol characteristics. Intriguingly,
P. brassicacearum
is closely related to
P. corrugata
, which is classified as an opportunistic phytopathogen. Twenty-one
P. brassicacearum
genomes have been sequenced to date. In the current review, genomes of
P. brassicacearum
and strains from the
P. corrugata
clade were mined for regions associated with PGP, biocontrol and pathogenicity. We discovered that ‘beneficial’ bacteria and those classified as plant pathogens have many genes in common; thus, only a fine line separates beneficial/harmless commensals from those capable of causing disease in plants. The genotype and physiological state of the plant, the presence of biotic/abiotic stressors, and the ability of bacteria to manipulate the plant immune system collectively contribute to how the bacterial-plant interaction plays out. Because production of extracellular metabolites is energetically costly, these compounds are expected to impart a fitness advantage to the producer.
P. brassicacearum
is able to reduce the threat of nematode predation through release of metabolites involved in biocontrol. Moreover this bacterium has the unique ability to form biofilms on the head of Caenorhabditis elegans, as a second mechanism of predator avoidance. Rhizobacteria, plants, fungi, and microfaunal predators have occupied a shared niche for millions of years and, in many ways, they function as a single organism. Accordingly, it is essential that we appreciate the dynamic interplay among these members of the community.
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156
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Ossowicki A, Tracanna V, Petrus MLC, van Wezel G, Raaijmakers JM, Medema MH, Garbeva P. Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat. Proc Biol Sci 2020; 287:20192527. [PMID: 32070256 DOI: 10.1098/rspb.2019.2527] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
In disease-suppressive soils, microbiota protect plants from root infections. Bacterial members of this microbiota have been shown to produce specific molecules that mediate this phenotype. To date, however, studies have focused on individual suppressive soils and the degree of natural variability of soil suppressiveness remains unclear. Here, we screened a large collection of field soils for suppressiveness to Fusarium culmorum using wheat (Triticum aestivum) as a model host plant. A high variation of disease suppressiveness was observed, with 14% showing a clear suppressive phenotype. The microbiological basis of suppressiveness to F. culmorum was confirmed by gamma sterilization and soil transplantation. Amplicon sequencing revealed diverse bacterial taxonomic compositions and no specific taxa were found exclusively enriched in all suppressive soils. Nonetheless, co-occurrence network analysis revealed that two suppressive soils shared an overrepresented bacterial guild dominated by various Acidobacteria. In addition, our study revealed that volatile emission may contribute to suppression, but not for all suppressive soils. Our study raises new questions regarding the possible mechanistic variability of disease-suppressive phenotypes across physico-chemically different soils. Accordingly, we anticipate that larger-scale soil profiling, along with functional studies, will enable a deeper understanding of disease-suppressive microbiomes.
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Affiliation(s)
- Adam Ossowicki
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Vittorio Tracanna
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | | | - Gilles van Wezel
- Institute of Biology, University of Leiden, Leiden, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Institute of Biology, University of Leiden, Leiden, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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157
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Core Rhizosphere Microbiomes of Dryland Wheat Are Influenced by Location and Land Use History. Appl Environ Microbiol 2020; 86:AEM.02135-19. [PMID: 31862727 DOI: 10.1128/aem.02135-19] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/10/2019] [Indexed: 01/22/2023] Open
Abstract
The Inland Pacific Northwest is one of the most productive dryland wheat production areas in the United States. We explored the bacterial and fungal communities associated with wheat in a controlled greenhouse experiment using soils from multiple locations to identify core taxa consistently associated with wheat roots and how land use history influences wheat-associated communities. Further, we examined microbial co-occurrence networks from wheat rhizospheres to identify candidate hub taxa. Location of origin and land use history (long-term no-till versus noncropped Conservation Reserve Program [CRP]) of soils were the strongest drivers of bacterial and fungal communities. Wheat rhizospheres were especially enriched in many bacterial families, while only a few fungal taxa were enriched in the rhizosphere. There was a core set of bacteria and fungi that was found in >95% of rhizosphere or bulk soil samples, including members of Bradyrhizobium, Sphingomonadaceae, Massilia, Variovorax, Oxalobacteraceae, and Caulobacteraceae Core fungal taxa in the rhizosphere included Nectriaceae, Ulocladium, Alternaria, Mortierella, and Microdochium Overall, there were fewer core fungal taxa, and the rhizosphere effect was not as pronounced as with bacteria. Cross-domain co-occurrence networks were used to identify hub taxa in the wheat rhizosphere, which included bacterial and fungal taxa (e.g., Sphingomonas, Massilia, Knufia, and Microdochium). Our results suggest that there is a relatively small group of core rhizosphere bacteria that were highly abundant on wheat roots regardless of soil origin and land use history. These core communities may play important roles in nutrient uptake, suppressing fungal pathogens, and other plant health functions.IMPORTANCE Plant-associated microbiomes are critical for plant health and other important agroecosystem processes. We assessed the bacterial and fungal microbiomes of wheat grown in soils from across a dryland wheat cropping systems in eastern Washington to identify the core microbiome on wheat roots that is consistent across soils from different locations and land use histories. Moreover, cross-domain co-occurrence network analysis identified core and hub taxa that may play important roles in microbial community assembly. Candidate core and hub taxa provide a starting point for targeting microbiome components likely to be critical to plant health and for constructing synthetic microbial communities for further experimentation. This work is one of the first examples of identifying a core microbiome on a major field crop grown across hundreds of square kilometers over a wide range of biogeographical zones.
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158
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Ali S, Hameed S, Shahid M, Iqbal M, Lazarovits G, Imran A. Functional characterization of potential PGPR exhibiting broad-spectrum antifungal activity. Microbiol Res 2020; 232:126389. [DOI: 10.1016/j.micres.2019.126389] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/21/2019] [Accepted: 11/29/2019] [Indexed: 02/03/2023]
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159
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Wang Y, Wang C, Gu Y, Wang P, Song W, Ma J, Yang X. The variability of bacterial communities in both the endosphere and ectosphere of different niches in Chinese chives (Allium tuberosum). PLoS One 2020; 15:e0227671. [PMID: 31945106 PMCID: PMC6964972 DOI: 10.1371/journal.pone.0227671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/24/2019] [Indexed: 12/18/2022] Open
Abstract
Deciphering the various types of interactions between plants and their microbiomes is a hot topic for research in ecology as well as in plant sciences and agronomy. To analyse and compare the differences in microbial communities in different compartments of Chinese chives, high-throughput sequencing technology was employed to amplify and sequence the V5-V6 region of the 16S rDNA of microorganisms in the leaves, phylloplanes, stems, roots and rhizospheres of Chinese chives. The sequences were clustered by operational taxonomic units (OTUs), and the community composition of bacteria between the endosphere (inner tissues) and ectosphere (outer surfaces) of Chinese chives was analysed based on the OTU. Overall, the results indicated that the endophytic bacteria in Chinese chives mainly include Proteobacteria, Actinobacteria, and Actinomycetes. Alpha diversity index analysis and OTU number analysis showed that the bacterial diversity and richness of the underground plant compartments were higher than those of the above-ground parts. PCoA based on the OTU level showed that the vertical stratification structure of plants and compartments had significant effects on the bacterial community structure. The richness of endophytic bacteria also varied greatly among the different varieties of Chinese chive. A considerable number of endophytic bacteria form symbiotic and mutually beneficial relationships with host plants, which play an important role in regulating host growth, metabolism and stress resistance. Further investigations are needed to uncover the evolution of interactions between plants and endophytes.
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Affiliation(s)
- Yuxin Wang
- College of Water Resources & Civil Engineering, China Agricultural University, Haidian, Beijing, China
- * E-mail:
| | - Chaonan Wang
- College of Water Resources & Civil Engineering, China Agricultural University, Haidian, Beijing, China
| | - Yizhu Gu
- College of Water Resources & Civil Engineering, China Agricultural University, Haidian, Beijing, China
| | - Pingzhi Wang
- College of Water Resources & Civil Engineering, China Agricultural University, Haidian, Beijing, China
| | - Weitang Song
- College of Water Resources & Civil Engineering, China Agricultural University, Haidian, Beijing, China
| | - Jinhai Ma
- Henan Jiuxing Institute of Biotechnology, Pingdingshan, Henan, China
| | - Xiaofei Yang
- Henan Jiuxing Institute of Biotechnology, Pingdingshan, Henan, China
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160
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Chitnis VR, Suryanarayanan TS, Nataraja KN, Prasad SR, Oelmüller R, Shaanker RU. Fungal Endophyte-Mediated Crop Improvement: The Way Ahead. FRONTIERS IN PLANT SCIENCE 2020; 11:561007. [PMID: 33193487 PMCID: PMC7652991 DOI: 10.3389/fpls.2020.561007] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/28/2020] [Indexed: 05/05/2023]
Abstract
Endophytes are non-disease causing microbes (bacteria and fungi) surviving in living tissues of plants. Their intimate association and possible coevolution with their plant partners have resulted in them contributing to an array of plant growth benefits ranging from enhanced growth and biomass accumulation, tolerance to abiotic and biotic stresses and in nutrient acquisition. The last couple of decades have witnessed a burgeoning literature on the role of endophytes (Class 3 type) in regulating plant growth and development and their adaptation to abiotic and biotic stresses. Though the underlying mechanisms of plant-endophyte interactions are far from clear, several studies have raised the hope of their potential application in agriculture, especially in mitigating abiotic and biotic stresses. The use of endophytes is envisaged as a route to reduce the production cost and burden on the environment by lessening the dependence on breeding for crop improvement and agrochemicals. Unfortunately, save a few well documented examples of their use, a little of these insights has been translated into actual agricultural applications. Here, we reflect on this paucity and elaborate on some of the important bottlenecks that might stand in way of fully realizing the potential that endophytes hold for crop improvement. We stress the need to study various facets of the endophyte-plant association for their gainful application in agriculture.
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Affiliation(s)
- Vijaya R. Chitnis
- School of Ecology and Conservation, University of Agricultural Sciences, GKVK, Bangalore, India
- *Correspondence: Vijaya R. Chitnis,
| | - Trichur S. Suryanarayanan
- Vivekananda Institute of Tropical Mycology (VINSTROM), Ramakrishna Mission Vidyapith, Chennai, India
| | - Karaba N. Nataraja
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore, India
| | - S. Rajendra Prasad
- Department of Seed Science and Technology, University of Agricultural Sciences, GKVK, Bangalore, India
| | - Ralf Oelmüller
- Plant Physiology, Matthias-Schleiden Institute, Friedrich-Schiller – University, Jena, Germany
| | - R. Uma Shaanker
- School of Ecology and Conservation, University of Agricultural Sciences, GKVK, Bangalore, India
- Vivekananda Institute of Tropical Mycology (VINSTROM), Ramakrishna Mission Vidyapith, Chennai, India
- R. Uma Shaanker,
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161
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Garcia J, Kao‐Kniffin J. Can dynamic network modelling be used to identify adaptive microbiomes? Funct Ecol 2019. [DOI: 10.1111/1365-2435.13491] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Joshua Garcia
- School of Integrative Plant Science Cornell University Ithaca NY USA
| | - Jenny Kao‐Kniffin
- School of Integrative Plant Science Cornell University Ithaca NY USA
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162
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Haarith D, Hu W, Kim DG, Showalter DN, Chen S, Bushley KE. Culturable mycobiome of soya bean cyst nematode (Heterodera glycines) cysts from a long-term soya bean-corn rotation system is dominated by Fusarium. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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163
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Bruisson S, Zufferey M, L'Haridon F, Trutmann E, Anand A, Dutartre A, De Vrieze M, Weisskopf L. Endophytes and Epiphytes From the Grapevine Leaf Microbiome as Potential Biocontrol Agents Against Phytopathogens. Front Microbiol 2019; 10:2726. [PMID: 31849878 PMCID: PMC6895011 DOI: 10.3389/fmicb.2019.02726] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/08/2019] [Indexed: 01/31/2023] Open
Abstract
Plants harbor diverse microbial communities that colonize both below-ground and above-ground organs. Some bacterial members of these rhizosphere and phyllosphere microbial communities have been shown to contribute to plant defenses against pathogens. In this study, we characterize the pathogen-inhibiting potential of 78 bacterial isolates retrieved from endophytic and epiphytic communities living in the leaves of three grapevine cultivars. We selected two economically relevant pathogens, the fungus Botrytis cinerea causing gray mold and the oomycete Phytophthora infestans, which we used as a surrogate for Plasmopara viticola causing downy mildew. Our results showed that epiphytic isolates were phylogenetically more diverse than endophytic isolates, the latter mostly consisting of Bacillus and Staphylococcus strains, but that mycelial inhibition of both pathogens through bacterial diffusible metabolites was more widespread among endophytes than among epiphytes. Six closely related Bacillus strains induced strong inhibition (>60%) of Botrytis cinerea mycelial growth. Among these, five led to significant perturbation in spore germination, ranging from full inhibition to reduction in germination rate and germ tube length. Different types of spore developmental anomalies were observed for different strains, suggesting multiple active compounds with different modes of action on this pathogen. Compared with B. cinerea, the oomycete P. infestans was inhibited in its mycelial growth by a higher number and more diverse group of isolates, including many Bacillus but also Variovorax, Pantoea, Staphylococcus, Herbaspirillum, or Sphingomonas strains. Beyond mycelial growth, both zoospore and sporangia germination were strongly perturbed upon exposure to cells or cell-free filtrates of selected isolates. Moreover, three strains (all epiphytes) inhibited the pathogen's growth via the emission of volatile compounds. The comparison of the volatile profiles of two of these active strains with those of two phylogenetically closely related, inactive strains led to the identification of molecules possibly involved in the observed volatile-mediated pathogen growth inhibition, including trimethylpyrazine, dihydrochalcone, and L-dihydroxanthurenic acid. This work demonstrates that grapevine leaves are a rich source of bacterial antagonists with strong inhibition potential against two pathogens of high economical relevance. It further suggests that combining diffusible metabolite-secreting endophytes with volatile-emitting epiphytes might be a promising multi-layer strategy for biological control of above-ground pathogens.
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Affiliation(s)
| | - Mónica Zufferey
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | - Eva Trutmann
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Abhishek Anand
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Agnès Dutartre
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Mout De Vrieze
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Laure Weisskopf
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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164
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Li M, Wang Q, Liu Z, Pan X, Zhang Y. Silicon application and related changes in soil bacterial community dynamics reduced ginseng black spot incidence in Panax ginseng in a short-term study. BMC Microbiol 2019; 19:263. [PMID: 31771526 PMCID: PMC6880445 DOI: 10.1186/s12866-019-1627-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/28/2019] [Indexed: 02/08/2023] Open
Abstract
Background This study analyzed the effect of silicon (Si) application on the occurrence of ginseng black spot caused by Alternaria panax. We explored the differences in soil physical and chemical factors and microbial community structure following Si application as well as the key factors that affected the occurrence of ginseng black spot in soil. Potted Panax ginseng plants were used to assess the effect of Si treatment on ginseng black spot. Soil physical and chemical properties were comprehensively analyzed. Bacterial communities were analyzed using Illumina HiSeq sequencing targeting the 16S rRNA gene. Results After inoculation with A. panax, the morbidity (and morbidity index) of ginseng with and without Si was 52% (46) and 83% (77), respectively. Soil physical and chemical analysis showed that under the ginseng black spot inoculation, bacterial communities were mainly affected by pH and available potassium, followed by ammonium nitrogen and available Si. NMDS and PLS-DA analyses and the heat maps of relative abundance revealed that Si application elevated the resistance of ginseng black spot as regulated by the abundance and diversity of bacterial flora in rhizosphere soils. Heatmap analysis at the genus level revealed that A. panax + Si inoculations significantly increased the soil community abundance of Sandaracinus, Polycyclovorans, Hirschia, Haliangium, Nitrospira, Saccharothrix, Aeromicrobium, Luteimonas, and Rubellimicrobium and led to a bacterial community structure with relative abundances that were significantly similar to that of untreated soil. Conclusions Short-term Si application also significantly regulated the structural impact on soil microorganisms caused by ginseng black spot. Our findings indicated that Si applications may possibly be used in the prevention and treatment of ginseng black spot.
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Affiliation(s)
- Meijia Li
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agriculture Sciences, Changchun, 130112, People's Republic of China
| | - Qiuxia Wang
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agriculture Sciences, Changchun, 130112, People's Republic of China
| | - Zhengbo Liu
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agriculture Sciences, Changchun, 130112, People's Republic of China
| | - Xiaoxi Pan
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agriculture Sciences, Changchun, 130112, People's Republic of China
| | - Yayu Zhang
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agriculture Sciences, Changchun, 130112, People's Republic of China.
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165
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Testa S, Berger S, Piccardi P, Oechslin F, Resch G, Mitri S. Spatial structure affects phage efficacy in infecting dual-strain biofilms of Pseudomonas aeruginosa. Commun Biol 2019; 2:405. [PMID: 31701033 PMCID: PMC6828766 DOI: 10.1038/s42003-019-0633-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/26/2019] [Indexed: 12/12/2022] Open
Abstract
Bacterial viruses, or phage, are key members of natural microbial communities. Yet much research on bacterial-phage interactions has been conducted in liquid cultures involving single bacterial strains. Here we explored how bacterial diversity affects the success of lytic phage in structured communities. We infected a sensitive Pseudomonas aeruginosa strain PAO1 with a lytic phage Pseudomonas 352 in the presence versus absence of an insensitive P. aeruginosa strain PA14, in liquid culture versus colonies on agar. We found that both in liquid and in colonies, inter-strain competition reduced resistance evolution in the susceptible strain and decreased phage population size. However, while all sensitive bacteria died in liquid, bacteria in colonies could remain sensitive yet escape phage infection, due mainly to reduced growth in colony centers. In sum, spatial structure can protect bacteria against phage infection, while the presence of competing strains reduces the evolution of resistance to phage.
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Affiliation(s)
- Samuele Testa
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Sarah Berger
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Philippe Piccardi
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Frank Oechslin
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec City, QC Canada
| | - Grégory Resch
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
- Swiss Institute for Bioinformatics, Lausanne, Switzerland
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166
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Saleem M, Hu J, Jousset A. More Than the Sum of Its Parts: Microbiome Biodiversity as a Driver of Plant Growth and Soil Health. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2019. [DOI: 10.1146/annurev-ecolsys-110617-062605] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microorganisms drive several processes needed for robust plant growth and health. Harnessing microbial functions is thus key to productive and sustainable food production. Molecular methods have led to a greater understanding of the soil microbiome composition. However, translating species or gene composition into microbiome functionality remains a challenge. Community ecology concepts such as the biodiversity–ecosystem functioning framework may help predict the assembly and function of plant-associated soil microbiomes. Higher diversity can increase the number and resilience of plant-beneficial functions that can be coexpressed and unlock the expression of plant-beneficial traits that are hard to obtain from any species in isolation. We combine well-established community ecology concepts with molecular microbiology into a workable framework that may enable us to predict and enhance soil microbiome functionality to promote robust plant growth in a global change context.
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Affiliation(s)
- Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, Alabama 36104, USA
| | - Jie Hu
- Institute of Environmental Biology, Ecology and Biodiversity, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Alexandre Jousset
- Institute of Environmental Biology, Ecology and Biodiversity, Utrecht University, 3584 CH Utrecht, The Netherlands
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167
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Affiliation(s)
- Susannah G. Tringe
- U.S. Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598, USA
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168
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Inhibitory interaction networks among coevolved Streptomyces populations from prairie soils. PLoS One 2019; 14:e0223779. [PMID: 31671139 PMCID: PMC6822729 DOI: 10.1371/journal.pone.0223779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/29/2019] [Indexed: 12/24/2022] Open
Abstract
Soil microbes live within highly complex communities, where community composition, function, and evolution are the product of diverse interactions among community members. Analysis of the complex networks of interactions within communities has the potential to shed light on community stability, functioning, and evolution. However, we have little understanding of the variation in interaction networks among coevolved soil populations. We evaluated networks of antibiotic inhibitory interactions among sympatric Streptomyces communities from prairie soil. Inhibition networks differed significantly in key network characteristics from expectations under null models, largely reflecting variation among Streptomyces in the number of sympatric populations that they inhibited. Moreover, networks of inhibitory interactions within Streptomyces communities differed significantly from each other, suggesting unique network structures among soil communities from different locations. Analyses of tri-partite interactions (triads) showed that some triads were significantly over- or under- represented, and that communities differed in ‘preferred’ triads. These results suggest that local processes generate distinct structures among sympatric Streptomyces inhibition networks in soil. Understanding the properties of microbial interaction networks that generate competitive and functional capacities of soil communities will shed light on the ecological and coevolutionary history of sympatric populations, and provide a foundation for more effective management of inhibitory capacities of soil microbial communities.
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169
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Agnolucci M, Palla M, Cristani C, Cavallo N, Giovannetti M, De Angelis M, Gobbetti M, Minervini F. Beneficial Plant Microorganisms Affect the Endophytic Bacterial Communities of Durum Wheat Roots as Detected by Different Molecular Approaches. Front Microbiol 2019; 10:2500. [PMID: 31736925 PMCID: PMC6834690 DOI: 10.3389/fmicb.2019.02500] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/17/2019] [Indexed: 11/18/2022] Open
Abstract
This study aimed at characterising the endophytic bacterial communities living in durum wheat roots, as affected by wheat cultivar and inoculation of the Arbuscular mycorrhizal fungus Funneliformis mosseae IMA1 and the wheat root endophytic bacterium Lactobacillus plantarum B.MD.R.A2. These microorganisms were inoculated, alone or in combination, in durum wheat (cultivars Odisseo and Saragolla). Non-inoculated plants of each cultivar represented the controls. Forty-three days after sowing, roots were deprived of the epiphytic microbiota and subjected to DNA extraction. The DNA was used as template in PCR-DGGE analysis of the 16S rRNA gene (variable region V3–V5) and 16S (region V1–V3) metagenetics. Odisseo and Saragolla root endophytic bacterial biotas differed for number of OTUs and composition. In detail, Pseudomonas was higher in Odisseo than in Saragolla. The inoculation of F. mosseae and L. plantarum increased the abundance of Pseudomonas, some Actinobacteria (e.g., Streptomyces, Microbacterium, two genera including several plant growth promoting (PGP) strains) and Bacteroidetes in both cultivars. However, the endophytic bacterial biota of Saragolla roots inoculated just with lactobacilli did not differ from that of the control. The inoculation of Saragolla with F. mosseae, alone or in combination with lactobacilli, led to higher abundance of Rhodococcus, belonging to Actinobacteria and encompassing PGP strains. First, this work showed that F. mosseae and L. plantarum shape the endophytic bacterial biota of durum wheat roots. Abundance of some OTUs was affected by the microbial inoculation, depending on the cultivar. This result represents a starting point for exploitation of beneficial endophytes of wheat roots.
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Affiliation(s)
- Monica Agnolucci
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Michela Palla
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Caterina Cristani
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Noemi Cavallo
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Manuela Giovannetti
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Marco Gobbetti
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Fabio Minervini
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
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170
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Kopecky J, Samkova Z, Sarikhani E, Kyselková M, Omelka M, Kristufek V, Divis J, Grundmann GG, Moënne-Loccoz Y, Sagova-Mareckova M. Bacterial, archaeal and micro-eukaryotic communities characterize a disease-suppressive or conducive soil and a cultivar resistant or susceptible to common scab. Sci Rep 2019; 9:14883. [PMID: 31619759 PMCID: PMC6796001 DOI: 10.1038/s41598-019-51570-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/28/2019] [Indexed: 12/20/2022] Open
Abstract
Control of common scab disease can be reached by resistant cultivars or suppressive soils. Both mechanisms are likely to translate into particular potato microbiome profiles, but the relative importance of each is not known. Here, microbiomes of bulk and tuberosphere soil and of potato periderm were studied in one resistant and one susceptible cultivar grown in a conducive and a suppressive field. Disease severity was suppressed similarly by both means yet, the copy numbers of txtB gene (coding for a pathogenicity determinant) were similar in both soils but higher in periderms of the susceptible cultivar from conducive soil. Illumina sequencing of 16S rRNA genes for bacteria (completed by 16S rRNA microarray approach) and archaea, and of 18S rRNA genes for micro-eukarytes showed that in bacteria, the more important was the effect of cultivar and diversity decreased from resistant cultivar to bulk soil to susceptible cultivar. The major changes occurred in proportions of Actinobacteria, Chloroflexi, and Proteobacteria. In archaea and micro-eukaryotes, differences were primarily due to the suppressive and conducive soil. The effect of soil suppressiveness × cultivar resistance depended on the microbial community considered, but differed also with respect to soil and plant nutrient contents particularly in N, S and Fe.
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Affiliation(s)
- Jan Kopecky
- Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovská 509, 161 06, Prague 6, Czech Republic
| | - Zuzana Samkova
- Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovská 509, 161 06, Prague 6, Czech Republic
| | - Ensyeh Sarikhani
- Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovská 509, 161 06, Prague 6, Czech Republic
| | - Martina Kyselková
- Biology Centre of the Czech Academy of Sciences, v. v. i., Institute of Soil Biology, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Marek Omelka
- Faculty of Mathematics and Physics, Department of Probability and Mathematical Statistics, Charles University, Sokolovská 83, 186 75, Prague 8, Czech Republic
| | - Vaclav Kristufek
- Biology Centre of the Czech Academy of Sciences, v. v. i., Institute of Soil Biology, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Jiri Divis
- Faculty of Agriculture, University of South Bohemia, Studentská 13, 370 05, České Budějovice, Czech Republic
| | - Geneviève G Grundmann
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Marketa Sagova-Mareckova
- Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovská 509, 161 06, Prague 6, Czech Republic. .,Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamycka 129, Prague 6, Czech Republic.
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171
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Lopes LD, Weisberg AJ, Davis EW, Varize CDS, Pereira e Silva MDC, Chang JH, Loper JE, Andreote FD. Genomic and metabolic differences between Pseudomonas putida populations inhabiting sugarcane rhizosphere or bulk soil. PLoS One 2019; 14:e0223269. [PMID: 31581220 PMCID: PMC6776310 DOI: 10.1371/journal.pone.0223269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 09/17/2019] [Indexed: 11/19/2022] Open
Abstract
Pseudomonas putida is one of 13 major groups of Pseudomonas spp. and contains numerous species occupying diverse niches and performing many functions such as plant growth promotion and bioremediation. Here we compared a set of 19 P. putida isolates obtained from sugarcane rhizosphere or bulk soil using a population genomics approach aiming to assess genomic and metabolic differences between populations from these habitats. Phylogenomics placed rhizosphere versus bulk soil strains in separate clades clustering with different type strains of the P. putida group. Multivariate analyses indicated that the rhizosphere and bulk soil isolates form distinct populations. Comparative genomics identified several genetic functions (GO-terms) significantly different between populations, including some exclusively present in the rhizosphere or bulk soil strains, such as D-galactonic acid catabolism and cellulose biosynthesis, respectively. The metabolic profiles of rhizosphere and bulk soil populations analyzed by Biolog Ecoplates also differ significantly, most notably by the higher oxidation of D-galactonic/D-galacturonic acid by the rhizosphere population. Accordingly, D-galactonate catabolism operon (dgo) was present in all rhizosphere isolates and absent in the bulk soil population. This study showed that sugarcane rhizosphere and bulk soil harbor different populations of P. putida and identified genes and functions potentially associated with their soil niches.
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Affiliation(s)
- Lucas Dantas Lopes
- Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
- * E-mail: (LDL); (FDA)
| | - Alexandra J. Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
| | - Edward W. Davis
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
| | - Camila de S. Varize
- Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Michele de C. Pereira e Silva
- Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
| | - Joyce E. Loper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
| | - Fernando D. Andreote
- Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
- * E-mail: (LDL); (FDA)
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172
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Franken P, Takken FLW, Rep M. Transcript accumulation in a trifold interaction gives insight into mechanisms of biocontrol. THE NEW PHYTOLOGIST 2019; 224:547-549. [PMID: 31545885 DOI: 10.1111/nph.16141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Philipp Franken
- Erfurt Research Centre for Horticultural Crops, University of Applied Sciences Erfurt, Kühnhäuser Straße 101, 99090, Erfurt, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Frank L W Takken
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Martijn Rep
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
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173
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Schlatter DC, Paul NC, Shah DH, Schillinger WF, Bary AI, Sharratt B, Paulitz TC. Biosolids and Tillage Practices Influence Soil Bacterial Communities in Dryland Wheat. MICROBIAL ECOLOGY 2019; 78:737-752. [PMID: 30796467 DOI: 10.1007/s00248-019-01339-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Class B biosolids are used in dryland wheat (Triticum aestivum L.) production in eastern Washington as a source of nutrients and to increase soil organic matter, but little is known about their effects on bacterial communities and potential for harboring human pathogens. Moreover, conservation tillage is promoted to reduce erosion and soil degradation. We explored the impacts of biosolids or synthetic fertilizer in combination with traditional (conventional) or conservation tillage on soil bacterial communities. Bacterial communities were characterized from fresh biosolids, biosolid aggregates embedded in soil, and soil after a second application of biosolids using high-throughput amplicon sequencing. Biosolid application significantly affected bacterial communities, even 4 years after their application. Bacteria in the families Clostridiaceae, Norcardiaceae, Anaerolinaceae, Dietziaceae, and Planococcaceae were more abundant in fresh biosolids, biosolid aggregates, and soils treated with biosolids than in synthetically fertilized soils. Taxa identified as Turcibacter, Dietzia, Clostridiaceae, and Anaerolineaceae were highly abundant in biosolid aggregates in the soil and likely originated from the biosolids. In contrast, Oxalobacteriaceae, Streptomyceteaceae, Janthinobacterium, Pseudomonas, Kribbella, and Bacillus were rare in the fresh biosolids, but relatively abundant in biosolid aggregates in the soil, and probably originated from the soil to colonize the substrate. However, tillage had relatively minor effects on bacterial communities, with only a small number of taxa differing in relative abundance between traditional and conventional tillage. Although biosolid-associated bacteria persisted in soil, potentially pathogenic taxa were extremely rare and no toxin genes for key groups (Salmonella, Clostridium) were detectable, suggesting that although fecal contamination was apparent via indicator taxa, pathogen populations had declined to low levels. Thus, biosolid amendments had profound effects on soil bacterial communities both by introducing gut- or digester-derived bacteria and by enriching potentially beneficial indigenous soil populations.
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Affiliation(s)
- Daniel C Schlatter
- Wheat Health, Genetics and Quality Research Unit, USDA-ARS, Pullman, WA, 99164, USA
| | - Narayan C Paul
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Devendra H Shah
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - William F Schillinger
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Andy I Bary
- Puyallup Research and Extension Center, Washington State University, Puyallup, WA, 98371, USA
| | - Brenton Sharratt
- Northwest Sustainable Agroecosystems Research Unit, USDA-ARS, Pullman, WA, 99164, USA
| | - Timothy C Paulitz
- Wheat Health, Genetics and Quality Research Unit, USDA-ARS, Pullman, WA, 99164, USA.
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174
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Bass D, Stentiford GD, Wang HC, Koskella B, Tyler CR. The Pathobiome in Animal and Plant Diseases. Trends Ecol Evol 2019; 34:996-1008. [PMID: 31522755 DOI: 10.1016/j.tree.2019.07.012] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 07/14/2019] [Accepted: 07/23/2019] [Indexed: 12/11/2022]
Abstract
A growing awareness of the diversity and ubiquity of microbes (eukaryotes, prokaryotes, and viruses) associated with larger 'host' organisms has led to the realisation that many diseases thought to be caused by one primary agent are the result of interactions between multiple taxa and the host. Even where a primary agent can be identified, its effect is often moderated by other symbionts. Therefore, the one pathogen-one disease paradigm is shifting towards the pathobiome concept, integrating the interaction of multiple symbionts, host, and environment in a new understanding of disease aetiology. Taxonomically, pathobiomes are variable across host species, ecology, tissue type, and time. Therefore, a more functionally driven understanding of pathobiotic systems is necessary, based on gene expression, metabolic interactions, and ecological processes.
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Affiliation(s)
- David Bass
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Barrack Road, The Nothe, Weymouth, DT4 8UB, UK; Sustainable Aquaculture Futures, University of Exeter, Exeter, EX4 4QD, UK; Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.
| | - Grant D Stentiford
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Barrack Road, The Nothe, Weymouth, DT4 8UB, UK; Sustainable Aquaculture Futures, University of Exeter, Exeter, EX4 4QD, UK
| | - Han-Ching Wang
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 70101, Taiwan; International Center for Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Charles R Tyler
- Sustainable Aquaculture Futures, University of Exeter, Exeter, EX4 4QD, UK; Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4HB, UK
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175
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Thomashow LS, Kwak YS, Weller DM. Root-associated microbes in sustainable agriculture: models, metabolites and mechanisms. PEST MANAGEMENT SCIENCE 2019; 75:2360-2367. [PMID: 30868729 DOI: 10.1002/ps.5406] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 06/09/2023]
Abstract
Since the discovery of penicillin in 1928 and throughout the 'age of antibiotics' from the 1940s until the 1980s, the detection of novel antibiotics was restricted by lack of knowledge about the distribution and ecology of antibiotic producers in nature. The discovery that a phenazine compound produced by Pseudomonas bacteria could suppress soilborne plant pathogens, and its recovery from rhizosphere soil in 1990, provided the first incontrovertible evidence that natural metabolites could control plant pathogens in the environment and opened a new era in biological control by root-associated rhizobacteria. More recently, the advent of genomics, the availability of highly sensitive bioanalytical instrumentation, and the discovery of protective endophytes have accelerated progress toward overcoming many of the impediments that until now have limited the exploitation of beneficial plant-associated microbes to enhance agricultural sustainability. Here, we present key developments that have established the importance of these microbes in the control of pathogens, discuss concepts resulting from the exploration of classical model systems, and highlight advances emerging from ongoing investigations. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Linda S Thomashow
- USDA, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Department of Plant Pathology, Washington State University, Pullman, WA, USA
| | - Youn-Sig Kwak
- Department of Plant Medicine and Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - David M Weller
- USDA, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Department of Plant Pathology, Washington State University, Pullman, WA, USA
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Kerdraon L, Barret M, Laval V, Suffert F. Differential dynamics of microbial community networks help identify microorganisms interacting with residue-borne pathogens: the case of Zymoseptoria tritici in wheat. MICROBIOME 2019; 7:125. [PMID: 31470910 PMCID: PMC6717385 DOI: 10.1186/s40168-019-0736-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/16/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND Wheat residues are a crucial determinant of the epidemiology of Septoria tritici blotch, as they support the sexual reproduction of the causal agent Zymoseptoria tritici. We aimed to characterize the effect of infection with this fungal pathogen on the microbial communities present on wheat residues and to identify microorganisms interacting with it. We used metabarcoding to characterize the microbiome associated with wheat residues placed outdoors, with and without preliminary Z. tritici inoculation, comparing the first set of residues in contact with the soil and a second set without contact with the soil, on four sampling dates in two consecutive years. RESULTS The diversity of the tested conditions, leading to the establishment of different microbial communities according to the origins of the constitutive taxa (plant only, or plant and soil), highlighted the effect of Z. tritici on the wheat residue microbiome. Several microorganisms were affected by Z. tritici infection, even after the disappearance of the pathogen. Linear discriminant analyses and ecological network analyses were combined to describe the communities affected by the infection. The number of fungi and bacteria promoted or inhibited by inoculation with Z. tritici decreased over time and was smaller for residues in contact with the soil. The interactions between the pathogen and other microorganisms appeared to be mostly indirect, despite the strong position of the pathogen as a keystone taxon in networks. Direct interactions with other members of the communities mostly involved fungi, including other wheat pathogens. Our results provide essential information about the alterations to the microbial community in wheat residues induced by the mere presence of a fungal pathogen, and vice versa. Species already described as beneficial or biocontrol agents were found to be affected by pathogen inoculation. CONCLUSIONS The strategy developed here can be viewed as a proof-of-concept focusing on crop residues as a particularly rich ecological compartment, with a high diversity of fungal and bacterial taxa originating from both the plant and soil compartments, and for Z. tritici-wheat as a model pathosystem. By revealing putative antagonistic interactions, this study paves the way for improving the biological control of residue-borne diseases.
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Affiliation(s)
- Lydie Kerdraon
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France.
| | - Matthieu Barret
- UMR IRHS, INRA, Agrocampus Ouest, Université d'Angers, 49071, Beaucouzé, France
| | - Valérie Laval
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Frédéric Suffert
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France.
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177
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Ciancio A, Pieterse CMJ, Mercado-Blanco J. Editorial: Harnessing Useful Rhizosphere Microorganisms for Pathogen and Pest Biocontrol - Second Edition. Front Microbiol 2019; 10:1935. [PMID: 31555222 PMCID: PMC6724568 DOI: 10.3389/fmicb.2019.01935] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/06/2019] [Indexed: 01/22/2023] Open
Affiliation(s)
- Aurelio Ciancio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Corné M J Pieterse
- Department of Biology, Science4Life, Utrecht University, Utrecht, Netherlands
| | - Jesús Mercado-Blanco
- Instituto de Agricultura Sostenible, Agencia Estatal Consejo Superior de Investigaciones Científicas, Córdoba, Spain
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Attwood GT, Wakelin SA, Leahy SC, Rowe S, Clarke S, Chapman DF, Muirhead R, Jacobs JME. Applications of the Soil, Plant and Rumen Microbiomes in Pastoral Agriculture. Front Nutr 2019; 6:107. [PMID: 31380386 PMCID: PMC6646666 DOI: 10.3389/fnut.2019.00107] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/27/2019] [Indexed: 12/14/2022] Open
Abstract
The production of dairy, meat, and fiber by ruminant animals relies on the biological processes occurring in soils, forage plants, and the animals' rumens. Each of these components has an associated microbiome, and these have traditionally been viewed as distinct ecosystems. However, these microbiomes operate under similar ecological principles and are connected via water, energy flows, and the carbon and nitrogen nutrient cycles. Here, we summarize the microbiome research that has been done in each of these three environments (soils, forage plants, animals' rumen) and investigate what additional benefits may be possible through understanding the interactions between the various microbiomes. The challenge for future research is to enhance microbiome function by appropriate matching of plant and animal genotypes with the environment to improve the output and environmental sustainability of pastoral agriculture.
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Affiliation(s)
| | | | | | - Suzanne Rowe
- Animal Science, AgResearch, Invermay, New Zealand
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179
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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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180
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Abstract
As abundant members of microbial communities, viruses impact microbial mortality, carbon and nutrient cycling, and food web dynamics. Although most of our information about viral communities comes from marine systems, evidence is mounting to suggest that viruses are similarly important in soil. As abundant members of microbial communities, viruses impact microbial mortality, carbon and nutrient cycling, and food web dynamics. Although most of our information about viral communities comes from marine systems, evidence is mounting to suggest that viruses are similarly important in soil. Here I outline soil viral metagenomic approaches and the current state of soil viral ecology as a field, and then I highlight existing knowledge gaps that we can begin to fill. We are poised to elucidate soil viral contributions to terrestrial ecosystem processes, considering: the full suite of potential hosts across trophic scales, the ecological impacts of different viral replication strategies, links to economically relevant outcomes like crop productivity, and measurable in situ virus-host population dynamics across spatiotemporal scales and environmental conditions. Soon, we will learn how soil viruses contribute to food webs linked to organic matter decomposition, carbon and nutrient cycling, greenhouse gas emissions, and agricultural productivity.
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181
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Abstract
Microorganisms colonizing plant surfaces and internal tissues provide a number of life-support functions for their host. Despite increasing recognition of the vast functional capabilities of the plant microbiome, our understanding of the ecology and evolution of the taxonomically hyperdiverse microbial communities is limited. Here, we review current knowledge of plant genotypic and phenotypic traits as well as allogenic and autogenic factors that shape microbiome composition and functions. We give specific emphasis to the impact of plant domestication on microbiome assembly and how insights into microbiomes of wild plant relatives and native habitats can contribute to reinstate or enrich for microorganisms with beneficial effects on plant growth, development, and health. Finally, we introduce new concepts and perspectives in plant microbiome research, in particular how community ecology theory can provide a mechanistic framework to unravel the interplay of distinct ecological processes-i.e., selection, dispersal, drift, diversification-that structure the plant microbiome.
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Affiliation(s)
- Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands;
| | - Francisco Dini-Andreote
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands;
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands; .,Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands; .,Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
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182
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Compant S, Samad A, Faist H, Sessitsch A. A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application. J Adv Res 2019; 19:29-37. [PMID: 31341667 PMCID: PMC6630030 DOI: 10.1016/j.jare.2019.03.004] [Citation(s) in RCA: 492] [Impact Index Per Article: 98.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/13/2019] [Accepted: 03/13/2019] [Indexed: 01/06/2023] Open
Abstract
Microbiota are important for plant growth, health and stress resilience. Inoculation with key microbiota members can improve plant traits. Tailored selection and delivery of microbial strains or consortia is required. Microbiome improvement may be achieved by appropriate agro-management practices. Plant breeding for improved interaction with microbiota will be of benefit.
Plants have evolved with a plethora of microorganisms having important roles for plant growth and health. A considerable amount of information is now available on the structure and dynamics of plant microbiota as well as on the functional capacities of isolated community members. Due to the interesting functional potential of plant microbiota as well as due to current challenges in crop production there is an urgent need to bring microbial innovations into practice. Different approaches for microbiome improvement exist. On the one hand microbial strains or strain combinations can be applied, however, field success is often variable and improvement is urgently required. Smart, knowledge-driven selection of microorganisms is needed as well as the use of suitable delivery approaches and formulations. On the other hand, farming practices or the plant genotype can influence plant microbiota and thus functioning. Therefore, selection of appropriate farming practices and plant breeding leading to improved plant-microbiome interactions are avenues to increase the benefit of plant microbiota. In conclusion, different avenues making use of a new generation of inoculants as well as the application of microbiome-based agro-management practices and improved plant lines could lead to a better use of the plant microbiome. This paper reviews the importance and functionalities of the bacterial plant microbiome and discusses challenges and concepts in regard to the application of plant-associated bacteria.
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Affiliation(s)
- Stéphane Compant
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources Unit, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - Abdul Samad
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources Unit, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - Hanna Faist
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources Unit, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources Unit, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
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183
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A Phylogenetic and Functional Perspective on Volatile Organic Compound Production by Actinobacteria. mSystems 2019; 4:mSystems00295-18. [PMID: 30863793 PMCID: PMC6401417 DOI: 10.1128/msystems.00295-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/08/2019] [Indexed: 01/01/2023] Open
Abstract
Soil microbes produce a diverse array of natural products, including volatile organic compounds (VOCs). Volatile compounds are important molecules in soil habitats, where they mediate interactions between bacteria, fungi, insects, plants, and animals. We measured the VOCs produced by a broad diversity of soil- and dust-dwelling Actinobacteria in vitro. We detected a total of 126 unique volatile compounds, and each strain produced a unique combination of VOCs. While some of the compounds were produced by many strains, most were strain specific. Importantly, VOC profiles were more similar between closely related strains, indicating that evolutionary and ecological processes generate predictable patterns of VOC production. Finally, we observed that actinobacterial VOCs had both stimulatory and inhibitory effects on the growth of bacteria that represent a plant-beneficial symbiont and a plant-pathogenic strain, information that may lead to the development of novel strategies for plant disease prevention. Soil microbes produce an immense diversity of metabolites, including volatile organic compounds (VOCs), which can shape the structure and function of microbial communities. VOCs mediate a multitude of microbe-microbe interactions, including antagonism. Despite their importance, the diversity and functional relevance of most microbial volatiles remain uncharacterized. We assembled a taxonomically diverse collection of 48 Actinobacteria isolated from soil and airborne dust and surveyed the VOCs produced by these strains on two different medium types in vitro using gas chromatography-mass spectrometry (GC-MS). We detected 126 distinct VOCs and structurally identified approximately 20% of these compounds, which were predominately C1 to C5 hetero-VOCs, including (oxygenated) alcohols, ketones, esters, and nitrogen- and sulfur-containing compounds. Each strain produced a unique VOC profile. While the most common VOCs were likely by-products of primary metabolism, most of the VOCs were strain specific. We observed a strong taxonomic and phylogenetic signal for VOC profiles, suggesting their role in finer-scale patterns of ecological diversity. Finally, we investigated the functional potential of these VOCs by assessing their effects on growth rates of both pathogenic and nonpathogenic pseudomonad strains. We identified sets of VOCs that correlated with growth inhibition and stimulation, information that may facilitate the development of microbial VOC-based pathogen control strategies. IMPORTANCE Soil microbes produce a diverse array of natural products, including volatile organic compounds (VOCs). Volatile compounds are important molecules in soil habitats, where they mediate interactions between bacteria, fungi, insects, plants, and animals. We measured the VOCs produced by a broad diversity of soil- and dust-dwelling Actinobacteria in vitro. We detected a total of 126 unique volatile compounds, and each strain produced a unique combination of VOCs. While some of the compounds were produced by many strains, most were strain specific. Importantly, VOC profiles were more similar between closely related strains, indicating that evolutionary and ecological processes generate predictable patterns of VOC production. Finally, we observed that actinobacterial VOCs had both stimulatory and inhibitory effects on the growth of bacteria that represent a plant-beneficial symbiont and a plant-pathogenic strain, information that may lead to the development of novel strategies for plant disease prevention.
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184
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Abstract
The manipulation and engineering of microbiomes could lead to improved human health, environmental sustainability, and agricultural productivity. However, microbiomes have proven difficult to alter in predictable ways, and their emergent properties are poorly understood. The history of biology has demonstrated the power of model systems to understand complex problems such as gene expression or development. Therefore, a defined and genetically tractable model community would be useful to dissect microbiome assembly, maintenance, and processes. We have developed a tractable model rhizosphere microbiome, designated THOR, containing Pseudomonas koreensis, Flavobacterium johnsoniae, and Bacillus cereus, which represent three dominant phyla in the rhizosphere, as well as in soil and the mammalian gut. The model community demonstrates emergent properties, and the members are amenable to genetic dissection. We propose that THOR will be a useful model for investigations of community-level interactions. The quest to manipulate microbiomes has intensified, but many microbial communities have proven to be recalcitrant to sustained change. Developing model communities amenable to genetic dissection will underpin successful strategies for shaping microbiomes by advancing an understanding of community interactions. We developed a model community with representatives from three dominant rhizosphere taxa, the Firmicutes, Proteobacteria, and Bacteroidetes. We chose Bacillus cereus as a model rhizosphere firmicute and characterized 20 other candidates, including “hitchhikers” that coisolated with B. cereus from the rhizosphere. Pairwise analysis produced a hierarchical interstrain-competition network. We chose two hitchhikers, Pseudomonas koreensis from the top tier of the competition network and Flavobacterium johnsoniae from the bottom of the network, to represent the Proteobacteria and Bacteroidetes, respectively. The model community has several emergent properties, induction of dendritic expansion of B. cereus colonies by either of the other members, and production of more robust biofilms by the three members together than individually. Moreover, P. koreensis produces a novel family of alkaloid antibiotics that inhibit growth of F. johnsoniae, and production is inhibited by B. cereus. We designate this community THOR, because the members are the hitchhikers of the rhizosphere. The genetic, genomic, and biochemical tools available for dissection of THOR provide the means to achieve a new level of understanding of microbial community behavior.
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185
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Brinkmann N, Schneider D, Sahner J, Ballauff J, Edy N, Barus H, Irawan B, Budi SW, Qaim M, Daniel R, Polle A. Intensive tropical land use massively shifts soil fungal communities. Sci Rep 2019; 9:3403. [PMID: 30833601 PMCID: PMC6399230 DOI: 10.1038/s41598-019-39829-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 01/30/2019] [Indexed: 12/02/2022] Open
Abstract
Soil fungi are key players in nutrient cycles as decomposers, mutualists and pathogens, but the impact of tropical rain forest transformation into rubber or oil palm plantations on fungal community structures and their ecological functions are unknown. We hypothesized that increasing land use intensity and habitat loss due to the replacement of the hyperdiverse forest flora by nonendemic cash crops drives a drastic loss of diversity of soil fungal taxa and impairs the ecological soil functions. Unexpectedly, rain forest conversion was not associated with strong diversity loss but with massive shifts in soil fungal community composition. Fungal communities clustered according to land use system and loss of plant species. Network analysis revealed characteristic fungal genera significantly associated with different land use systems. Shifts in soil fungal community structure were particularly distinct among different trophic groups, with substantial decreases in symbiotrophic fungi and increases in saprotrophic and pathotrophic fungi in oil palm and rubber plantations in comparison with rain forests. In conclusion, conversion of rain forests and current land use systems restructure soil fungal communities towards enhanced pathogen pressure and, thus, threaten ecosystem health functions.
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Affiliation(s)
- Nicole Brinkmann
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany.
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Goettingen, Göttingen, Germany
| | - Josephine Sahner
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
| | - Johannes Ballauff
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
| | - Nur Edy
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
- Department of Agrotechnology, Faculty of Agriculture, Tadulako University, Palu, Indonesia
| | - Henry Barus
- Department of Agrotechnology, Faculty of Agriculture, Tadulako University, Palu, Indonesia
| | - Bambang Irawan
- Department of Forestry, University of Jambi, Jambi, Indonesia
| | - Sri Wilarso Budi
- Department of Silviculture, Faculty of Forestry, Bogor Agriculture University, Bogor, Indonesia
| | - Matin Qaim
- Department of Agricultural Economics and Rural Development, University of Goettingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Goettingen, Göttingen, Germany
| | - Andrea Polle
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
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186
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El Mujtar V, Muñoz N, Prack Mc Cormick B, Pulleman M, Tittonell P. Role and management of soil biodiversity for food security and nutrition; where do we stand? GLOBAL FOOD SECURITY-AGRICULTURE POLICY ECONOMICS AND ENVIRONMENT 2019. [DOI: 10.1016/j.gfs.2019.01.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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187
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Toyota K, Shirai S. Growing Interest in Microbiome Research Unraveling Disease Suppressive Soils against Plant Pathogens. Microbes Environ 2019; 33:345-347. [PMID: 30606975 PMCID: PMC6307993 DOI: 10.1264/jsme2.me3304rh] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Koki Toyota
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology
| | - Sayo Shirai
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology
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188
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Hayden HL, Rochfort SJ, Ezernieks V, Savin KW, Mele PM. Metabolomics approaches for the discrimination of disease suppressive soils for Rhizoctonia solani AG8 in cereal crops using 1H NMR and LC-MS. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:1627-1638. [PMID: 30360288 DOI: 10.1016/j.scitotenv.2018.09.249] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 06/08/2023]
Abstract
The suppression of soilborne crop pathogens such as Rhizoctonia solani AG8 may offer a sustainable and enduring method for disease control, though soils with these properties are difficult to identify. In this study, we analysed the soil metabolic profiles of suppressive and non-suppressive soils over 2 years of cereal production. We collected bulk and rhizosphere soil at different cropping stages and subjected soil extracts to liquid chromatography-mass spectrometry (LC-MS) and proton nuclear magnetic resonance spectroscopy (1H NMR) analyses. Community analyses of suppressive and non-suppressive soils using principal component analyses and predictive modelling of LC-MS and NMR datasets respectively, revealed distinct biochemical profiles for the two soil types with clustering based on suppressiveness and cropping stage. NMR spectra revealed the suppressive soils to be more abundant in sugar molecules than non-suppressive soils, which were more abundant in lipids and terpenes. LC-MS features that were significantly more abundant in the suppressive soil were identified and assessed as potential biomarkers for disease suppression. The structures of a potential class of LC-MS biomarkers were elucidated using accurate mass data and MS fragmentation spectrum information. The most abundant compound found in association with suppressive soils was confirmed to be a macrocarpal, which is an antimicrobial secondary metabolite. Our study has demonstrated the utility of environmental metabolomics for the study of disease suppressive soils, resulting in the discovery of a macrocarpal biomarker for R. solani AG8 suppressive soil which can be further studied functionally in association with suppression pot trials and microbial isolation studies.
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Affiliation(s)
- Helen L Hayden
- Agriculture Victoria Research, Department of Economic Development, Jobs, Trade and Resources, 5 Ring Rd, Bundoora, Victoria 3083, Australia.
| | - Simone J Rochfort
- Agriculture Victoria Research, Department of Economic Development, Jobs, Trade and Resources, 5 Ring Rd, Bundoora, Victoria 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3083, Australia
| | - Vilnis Ezernieks
- Agriculture Victoria Research, Department of Economic Development, Jobs, Trade and Resources, 5 Ring Rd, Bundoora, Victoria 3083, Australia
| | - Keith W Savin
- Agriculture Victoria Research, Department of Economic Development, Jobs, Trade and Resources, 5 Ring Rd, Bundoora, Victoria 3083, Australia
| | - Pauline M Mele
- Agriculture Victoria Research, Department of Economic Development, Jobs, Trade and Resources, 5 Ring Rd, Bundoora, Victoria 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3083, Australia
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189
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Cruz-Paredes C, Svenningsen NB, Nybroe O, Kjøller R, Frøslev TG, Jakobsen I. Suppression of arbuscular mycorrhizal fungal activity in a diverse collection of non-cultivated soils. FEMS Microbiol Ecol 2019; 95:5305856. [DOI: 10.1093/femsec/fiz020] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/31/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Carla Cruz-Paredes
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Nanna Bygvraa Svenningsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Ole Nybroe
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Rasmus Kjøller
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Tobias Guldberg Frøslev
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Natural History Museum of Denmark, University of Copenhagen, Øster Volgade 5, 1350, Copenhagen, Denmark
| | - Iver Jakobsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
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190
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Baker JL, Edlund A. Exploiting the Oral Microbiome to Prevent Tooth Decay: Has Evolution Already Provided the Best Tools? Front Microbiol 2019; 9:3323. [PMID: 30687294 PMCID: PMC6338091 DOI: 10.3389/fmicb.2018.03323] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 12/20/2018] [Indexed: 12/22/2022] Open
Abstract
To compete in the relatively exposed oral cavity, resident microbes must avoid being replaced by newcomers. This selective constraint, coupled with pressure on the host to cultivate a beneficial microbiome, has rendered a commensal oral microbiota that displays colonization resistance, protecting the human host from invasive species, including pathogens. Rapid increases in carbohydrate consumption have disrupted the evolved homeostasis between the oral microbiota and dental health, reflected by the high prevalence of dental caries. Development of novel modalities to prevent caries has been the subject of a breadth of research. This mini review provides highlights of these endeavors and discusses the rationale and pitfalls behind the major avenues of approach. Despite efficacy, fluoride and other broad-spectrum interventions are unlikely to further reduce the incidence of dental caries. The most promising methodologies in development are those that exploit the exclusive nature of the healthy oral microbiome. Probiotics derived from the dental plaque of healthy individuals sharply antagonize cariogenic species, such as Streptococcus mutans. Meanwhile, targeted antimicrobials allow for the killing of specific pathogens, allowing reestablishment of a healthy microbiome, presumably with its protective effects. The oral microbiota manufactures a massive array of small molecules, some of which are correlated with health and are likely to antagonize pathogens. The prohibitive cost associated with sufficiently rigorous clinical trials, and the status of dental caries as a non-life-threatening condition will likely continue to impede the advancement of new therapeutics to market. Nevertheless, there is room for optimism, as it appears evolution may have already provided the best tools.
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Affiliation(s)
| | - Anna Edlund
- Genomic Medicine Group, J. Craig Venter Institute, La Jolla, CA, United States
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191
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Thomashow LS, LeTourneau MK, Kwak Y, Weller DM. The soil-borne legacy in the age of the holobiont. Microb Biotechnol 2019; 12:51-54. [PMID: 30328280 PMCID: PMC6302707 DOI: 10.1111/1751-7915.13325] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 09/17/2018] [Indexed: 11/30/2022] Open
Abstract
Future efforts to increase agricultural productivity will focus on crops as functional units comprised of plants and their associated microflora in the context of the various environments in which they are grown. It is suggested that future efforts to increase agricultural productivity will focus on crops as functional units comprised of plants and their associated beneficial microorganisms in the context in which they are grown. Scientists, industry, and farmers must work closely together to develop, adapt, and apply new technologies to a wide range of cropping systems. Consumer education is needed help grow public awareness that 'plant probiotics' offer a safe and environmentally friendly alternative to dependence on the use of chemical pesticides.
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Affiliation(s)
- Linda S. Thomashow
- Wheat Health, Genetics, and Quality Research UnitUnited States Department of AgricultureAgricultural Research ServicePullmanWA99164‐6430USA
| | - Melissa K. LeTourneau
- Wheat Health, Genetics, and Quality Research UnitUnited States Department of AgricultureAgricultural Research ServicePullmanWA99164‐6430USA
| | - Youn‐Sig Kwak
- Department of Plant Medicine and Institute of Agriculture & Life SciencesGyeongsang National UniversityJinju52828Korea
| | - David M. Weller
- Wheat Health, Genetics, and Quality Research UnitUnited States Department of AgricultureAgricultural Research ServicePullmanWA99164‐6430USA
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192
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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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193
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Assessing the resilience of biodiversity-driven functions in agroecosystems under environmental change. ADV ECOL RES 2019. [DOI: 10.1016/bs.aecr.2019.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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194
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Yang M, Mavrodi DV, Thomashow LS, Weller DM. Differential Response of Wheat Cultivars to Pseudomonas brassicacearum and Take-All Decline Soil. PHYTOPATHOLOGY 2018; 108:1363-1372. [PMID: 29905506 PMCID: PMC6483097 DOI: 10.1094/phyto-01-18-0024-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
2,4-Diacetylphloroglucinol (DAPG)-producing Pseudomonas spp. in the P. fluorescens complex are primarily responsible for a natural suppression of take-all of wheat known as take-all decline (TAD) in many fields in the United States. P. brassicacearum, the most common DAPG producer found in TAD soils in the Pacific Northwest (PNW) of the United States, has biological control, growth promoting and phytotoxic activities. In this study, we explored how the wheat cultivar affects the level of take-all suppression when grown in a TAD soil, and how cultivars respond to colonization by P. brassicacearum. Three cultivars (Tara, Finley, and Buchanan) supported similar rhizosphere population sizes of P. brassicacearum when grown in a TAD soil, however they developed significantly different amounts of take-all. Cultivars Tara and Buchanan developed the least and most take-all, respectively, and Finley showed an intermediate amount of disease. However, when grown in TAD soil that was pasteurized to eliminate both DAPG producers and take-all suppression, all three cultivars were equally susceptible to take-all. The three cultivars also responded differently to the colonization and phytotoxicity of P. brassicacearum strains Q8r1-96 and L5.1-96, which are characteristic of DAPG producers in PNW TAD soils. Compared with cultivar Tara, cultivar Buchanan showed significantly reduced seedling emergence and root growth when colonized by P. brassicacearum, and the response of Finley was intermediate. However, all cultivars emerged equally when treated with a DAPG-deficient mutant of Q8r1-96. Our results indicate that wheat cultivars grown in a TAD soil modulate both the robustness of take-all suppression and the potential phytotoxicity of the antibiotic DAPG.
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Affiliation(s)
| | - Dmitri V. Mavrodi
- Department of Cell and Molecular Biology, The University of Southern Mississippi, Hattiesburg 39406
| | - Linda S. Thomashow
- U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164-6430
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195
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Kwon YS, Jeon CW, Bae DW, Seo JS, Thomashow LS, Weller DM, Kwak YS. Construction of a proteome reference map and response of Gaeumannomyces graminis var. tritici to 2,4-diacetylphloroglucinol. Fungal Biol 2018; 122:1098-1108. [PMID: 30342625 DOI: 10.1016/j.funbio.2018.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/31/2018] [Accepted: 09/07/2018] [Indexed: 10/28/2022]
Abstract
Take-all disease, caused by Gaeumannomyces graminis var. tritici (Ggt), is one of the most serious root diseases in wheat production. In this study, a proteomic platform based on 2-dimensional gel electrophoresis (2-DE) and Matrix-Assisted Laser Desorption/Ionization Time of Flight Tandem Mass Spectrometry (MALDI-TOF/TOF MS) was used to construct the first proteome database reference map of G. graminis var. tritici and to identify the response of the pathogen to 2,4-diacetylphloroglucinol (DAPG), which is a natural antibiotic produced by antagonistic Pseudomonas spp. in take-all suppressive soils. For mapping, a total of 240 spots was identified that represented 209 different proteins. The most abundant biological function categories in the Ggt proteome were related to carbohydrate metabolism (21%), amino acid metabolism (15%), protein folding and degradation (12%), translation (11%), and stress response (10%). In total, 51 Ggt proteins were affected by DAPG treatment. Based on gene ontology, carbohydrate metabolism, amino acid metabolism, stress response, and protein folding and degradation proteins were the ones most modulated by DAPG treatment. This study provides the first extensive proteomic reference map constructed for Ggt and represents the first time that the response of Ggt to DAPG has been characterized at the proteomic level.
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Affiliation(s)
- Young Sang Kwon
- Environmental Toxicology Research Center, Korea Institute of Toxicology (KIT), Jinju 52834, Republic of Korea
| | - Chang-Wook Jeon
- Division of Applied Life Science (BK21Plus) and Institute of Agriculture & Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Dong-Won Bae
- Center for Research Facilities, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jong-Su Seo
- Environmental Toxicology Research Center, Korea Institute of Toxicology (KIT), Jinju 52834, Republic of Korea
| | - Linda S Thomashow
- United States Department of Agriculture-Agriculture Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164, USA
| | - David M Weller
- United States Department of Agriculture-Agriculture Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164, USA
| | - Youn-Sig Kwak
- Division of Applied Life Science (BK21Plus) and Institute of Agriculture & Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea.
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196
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Yuan J, Zhao J, Wen T, Zhao M, Li R, Goossens P, Huang Q, Bai Y, Vivanco JM, Kowalchuk GA, Berendsen RL, Shen Q. Root exudates drive the soil-borne legacy of aboveground pathogen infection. MICROBIOME 2018; 6:156. [PMID: 30208962 PMCID: PMC6136170 DOI: 10.1186/s40168-018-0537-x] [Citation(s) in RCA: 260] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/23/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND Plants are capable of building up beneficial rhizosphere communities as is evidenced by disease-suppressive soils. However, it is not known how and why soil bacterial communities are impacted by plant exposure to foliar pathogens and if such responses might improve plant performance in the presence of the pathogen. Here, we conditioned soil by growing multiple generations (five) of Arabidopsis thaliana inoculated aboveground with Pseudomonas syringae pv tomato (Pst) in the same soil. We then examined rhizosphere communities and plant performance in a subsequent generation (sixth) grown in pathogen-conditioned versus control-conditioned soil. Moreover, we assessed the role of altered root exudation profiles in shaping the root microbiome of infected plants. RESULTS Plants grown in conditioned soil showed increased levels of jasmonic acid and improved disease resistance. Illumina Miseq 16S rRNA gene tag sequencing revealed that both rhizosphere and bulk soil bacterial communities were altered by Pst infection. Infected plants exhibited significantly higher exudation of amino acids, nucleotides, and long-chain organic acids (LCOAs) (C > 6) and lower exudation levels for sugars, alcohols, and short-chain organic acids (SCOAs) (C ≤ 6). Interestingly, addition of exogenous amino acids and LCOA also elicited a disease-suppressive response. CONCLUSION Collectively, our data suggest that plants can recruit beneficial rhizosphere communities via modification of plant exudation patterns in response to exposure to aboveground pathogens to the benefit of subsequent plant generations.
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Affiliation(s)
- Jun Yuan
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization; National Engineering Research Center for Organic-based Fertilizers; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun Zhao
- School of Geography Science, Nanjing Normal University, Nanjing, 210021, China
| | - Tao Wen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization; National Engineering Research Center for Organic-based Fertilizers; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mengli Zhao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization; National Engineering Research Center for Organic-based Fertilizers; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rong Li
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization; National Engineering Research Center for Organic-based Fertilizers; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Pim Goossens
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Qiwei Huang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization; National Engineering Research Center for Organic-based Fertilizers; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing, 100101, China
| | - Jorge M Vivanco
- Department of Horticulture and Landscape Architecture and Center for Rhizosphere Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Roeland L Berendsen
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization; National Engineering Research Center for Organic-based Fertilizers; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China.
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197
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Chaluvadi S, Bennetzen JL. Species-Associated Differences in the Below-Ground Microbiomes of Wild and Domesticated Setaria. FRONTIERS IN PLANT SCIENCE 2018; 9:1183. [PMID: 30186294 PMCID: PMC6111228 DOI: 10.3389/fpls.2018.01183] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 07/24/2018] [Indexed: 05/08/2023]
Abstract
The rhizosphere microbiome is known to play a crucial role in promoting plant growth, partly by countering soil-borne phytoparasites and by improving nutrient uptake. The abundance and composition of the rhizosphere and root-associated microbiota are influenced by several factors, including plant species and genotype. We hypothesize that crop domestication might influence the composition and diversity of plant-associated microbiomes. We tested the contribution of domestication to the bacterial and archaeal root and soil composition associated with six genotypes of domesticated Setaria italica and four genotypes of its wild ancestor, S. viridis. The bacterial microbiome in the rhizoplane and root endophyte compartments, and the archaea in the endophyte compartment, showed major composition differences. For instance, members of the Betaproteobacteria and Firmicutes were overrepresented in S. italica root samples compared to S. viridis. Metagenomic analysis of samples that contained both root surface-bound (rhizoplane) and inside-root (endophytic) bacteria defined two unique microbial communities only associated with S. italica roots and one only associated with S. viridis roots. Root endophytic bacteria were found in six discernible communities, of which four were primarily on S. italica and two primarily on S. viridis. Among archaea, Methanobacteria, and Methanomicrobia exhibited species-associated differences in the rhizosphere and root compartments, but most detected archaea were not classified more specifically than at the level of phylum. These results indicate a host genetic contribution to the microbial composition in Setaria, and suggest that domestication has selected for specific associations in the root and in the rhizosphere.
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198
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Nutrient- and Dose-Dependent Microbiome-Mediated Protection against a Plant Pathogen. Curr Biol 2018; 28:2487-2492.e3. [PMID: 30057302 DOI: 10.1016/j.cub.2018.05.085] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 03/20/2018] [Accepted: 05/29/2018] [Indexed: 12/22/2022]
Abstract
Plant-associated microbial communities can promote plant nutrient uptake, growth, and resistance to pathogens [1-3]. Host resistance to infection can increase directly through commensal-pathogen interactions or indirectly through modulation of host defenses [4-6], the mechanisms of which are best described for rhizosphere-associated bacteria. For example, Arabidopsis plants infected with the foliar pathogen, Pseudomonas syringae pathovar tomato (Pst), increase their root secretion of malate, which attracts Bacillus subtillis to the roots and leads to a stronger host response against Pst [7]. Although there are numerous examples of individual defensive symbionts (e.g., [8]), it is less clear whether this type of protection is an emergent property of whole microbial communities. In particular, relatively little is known about whether and how the presence of phyllosphere (above-ground) microbial communities can increase host resistance against pathogens. In this study, we examined the ability of augmented tomato phyllosphere microbiomes to confer resistance against the causal agent of bacterial speck, Pst. Across five independent experiments, the augmented phyllosphere microbiome was found to decrease pathogen colonization. Furthermore, the dose of commensal bacteria applied affected the degree of protection conferred, and although the effect is dependent on microbial composition, it is not clearly related to overall bacterial diversity. Finally, our results suggest that resources available to the phyllosphere microbial community may play an important role in protection, as the addition of fertilizer abolished the observed microbiome-mediated protection. Together, these results have clear relevance to microbiome-mediated protection within agricultural settings and the use of plant probiotics to increase disease resistance.
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199
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Peralta AL, Sun Y, McDaniel MD, Lennon JT. Crop rotational diversity increases disease suppressive capacity of soil microbiomes. Ecosphere 2018. [DOI: 10.1002/ecs2.2235] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Ariane L. Peralta
- Department of Biology East Carolina University S301B Howell Science Complex Greenville North Carolina 27858 USA
| | - Yanmei Sun
- Department of Biology East Carolina University S301B Howell Science Complex Greenville North Carolina 27858 USA
- School of Environment and Civil Engineering Dongguan University of Technology Dongguang 523808 China
| | - Marshall D. McDaniel
- Department of Agronomy Iowa State University 2517 Agronomy Hall Ames Iowa 50014 USA
| | - Jay T. Lennon
- Department of Biology Indiana University 261 Jordan Hall Bloomington Indiana 47405 USA
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200
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Hayden HL, Savin KW, Wadeson J, Gupta VVSR, Mele PM. Comparative Metatranscriptomics of Wheat Rhizosphere Microbiomes in Disease Suppressive and Non-suppressive Soils for Rhizoctonia solani AG8. Front Microbiol 2018; 9:859. [PMID: 29780371 PMCID: PMC5945926 DOI: 10.3389/fmicb.2018.00859] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/13/2018] [Indexed: 11/29/2022] Open
Abstract
The soilborne fungus Rhizoctonia solani anastomosis group (AG) 8 is a major pathogen of grain crops resulting in substantial production losses. In the absence of resistant cultivars of wheat or barley, a sustainable and enduring method for disease control may lie in the enhancement of biological disease suppression. Evidence of effective biological control of R. solani AG8 through disease suppression has been well documented at our study site in Avon, South Australia. A comparative metatranscriptomic approach was applied to assess the taxonomic and functional characteristics of the rhizosphere microbiome of wheat plants grown in adjacent fields which are suppressive and non-suppressive to the plant pathogen R. solani AG8. Analysis of 12 rhizosphere metatranscriptomes (six per field) was undertaken using two bioinformatic approaches involving unassembled and assembled reads. Differential expression analysis showed the dominant taxa in the rhizosphere based on mRNA annotation were Arthrobacter spp. and Pseudomonas spp. for non-suppressive samples and Stenotrophomonas spp. and Buttiauxella spp. for the suppressive samples. The assembled metatranscriptome analysis identified more differentially expressed genes than the unassembled analysis in the comparison of suppressive and non-suppressive samples. Suppressive samples showed greater expression of a polyketide cyclase, a terpenoid biosynthesis backbone gene (dxs) and many cold shock proteins (csp). Non-suppressive samples were characterised by greater expression of antibiotic genes such as non-heme chloroperoxidase (cpo) which is involved in pyrrolnitrin synthesis, and phenazine biosynthesis family protein F (phzF) and its transcriptional activator protein (phzR). A large number of genes involved in detoxifying reactive oxygen species (ROS) and superoxide radicals (sod, cat, ahp, bcp, gpx1, trx) were also expressed in the non-suppressive rhizosphere samples most likely in response to the infection of wheat roots by R. solani AG8. Together these results provide new insight into microbial gene expression in the rhizosphere of wheat in soils suppressive and non-suppressive to R. solani AG8. The approach taken and the genes involved in these functions provide direction for future studies to determine more precisely the molecular interplay of plant-microbe-pathogen interactions with the ultimate goal of the development of management options that promote beneficial rhizosphere microflora to reduce R. solani AG8 infection of crops.
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Affiliation(s)
- Helen L Hayden
- Department of Economic Development, Jobs, Transport and Resources, Agriculture Victoria Research, AgriBio, Bundoora, VIC, Australia
| | - Keith W Savin
- Department of Economic Development, Jobs, Transport and Resources, Agriculture Victoria Research, AgriBio, Bundoora, VIC, Australia
| | - Jenny Wadeson
- Department of Economic Development, Jobs, Transport and Resources, Agriculture Victoria Research, AgriBio, Bundoora, VIC, Australia
| | - Vadakattu V S R Gupta
- CSIRO Agriculture and Food, Glen Osmond, SA, Australia.,College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Pauline M Mele
- Department of Economic Development, Jobs, Transport and Resources, Agriculture Victoria Research, AgriBio, Bundoora, VIC, Australia.,School of Applied Systems Biology, La Trobe University, Melbourne, VIC, Australia
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