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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. Sci Total Environ 2019; 651:1627-1638. [PMID: 30360288 DOI: 10.1016/j.scitotenv.2018.09.249] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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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: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Bissett A, Fitzgerald A, Court L, Meintjes T, Mele PM, Reith F, Dennis PG, Breed MF, Brown B, Brown MV, Brugger J, Byrne M, Caddy-Retalic S, Carmody B, Coates DJ, Correa C, Ferrari BC, Gupta VVSR, Hamonts K, Haslem A, Hugenholtz P, Karan M, Koval J, Lowe AJ, Macdonald S, McGrath L, Martin D, Morgan M, North KI, Paungfoo-Lonhienne C, Pendall E, Phillips L, Pirzl R, Powell JR, Ragan MA, Schmidt S, Seymour N, Snape I, Stephen JR, Stevens M, Tinning M, Williams K, Yeoh YK, Zammit CM, Young A. Erratum to: Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database. Gigascience 2017; 6:3806414. [PMID: 30137319 PMCID: PMC5437940 DOI: 10.1093/gigascience/gix021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Bissett A, Fitzgerald A, Court L, Meintjes T, Mele PM, Reith F, Dennis PG, Breed MF, Brown B, Brown MV, Brugger J, Byrne M, Caddy-Retalic S, Carmody B, Coates DJ, Correa C, Ferrari BC, Gupta VVSR, Hamonts K, Haslem A, Hugenholtz P, Karan M, Koval J, Lowe AJ, Macdonald S, McGrath L, Martin D, Morgan M, North KI, Paungfoo-Lonhienne C, Pendall E, Phillips L, Pirzl R, Powell JR, Ragan MA, Schmidt S, Seymour N, Snape I, Stephen JR, Stevens M, Tinning M, Williams K, Yeoh YK, Zammit CM, Young A. Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database. Gigascience 2016; 5:21. [PMID: 27195106 PMCID: PMC4870752 DOI: 10.1186/s13742-016-0126-5] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 05/02/2016] [Indexed: 01/27/2023] Open
Abstract
Background Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The ‘Biomes of Australian Soil Environments’ (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function. Findings BASE currently provides amplicon sequences and associated contextual data for over 900 sites encompassing all Australian states and territories, a wide variety of bioregions, vegetation and land-use types. Amplicons target bacteria, archaea and general and fungal-specific eukaryotes. The growing database will soon include metagenomics data. Data are provided in both raw sequence (FASTQ) and analysed OTU table formats and are accessed via the project’s data portal, which provides a user-friendly search tool to quickly identify samples of interest. Processed data can be visually interrogated and intersected with other Australian diversity and environmental data using tools developed by the ‘Atlas of Living Australia’. Conclusions Developed within an open data framework, the BASE project is the first Australian soil microbial diversity database. The database will grow and link to other global efforts to explore microbial, plant, animal, and marine biodiversity. Its design and open access nature ensures that BASE will evolve as a valuable tool for documenting an often overlooked component of biodiversity and the many microbe-driven processes that are essential to sustain soil function and ecosystem services.
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Affiliation(s)
- Andrew Bissett
- CSIRO, Oceans and Atmosphere, Hobart, Tasmania Australia
| | | | | | - Thys Meintjes
- Centre for Comparative Genomics, Murdoch University, Perth, Western Australia Australia
| | - Pauline M Mele
- Victorian Department of Economic Development, Jobs, Transport and Resources and La Trobe University, Agribio Centre, Bundoora, Victoria 3083 Australia
| | - Frank Reith
- CSIRO Land and Water, Adelaide, South Australia Australia ; School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace Adelaide, South Australia 5005 Australia
| | - Paul G Dennis
- School of Agriculture and Food Science, The University of Queensland, St Lucia, Queensland 4072 Australia
| | - Martin F Breed
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace Adelaide, South Australia 5005 Australia
| | - Belinda Brown
- Parks Australia, Department of the Environment, Canberra, ACT 2601 Australia
| | - Mark V Brown
- School of Biotechnology and Biomolecular Sciences, UNSW Australia, Sydney, New South Wales 2052 Australia
| | - Joel Brugger
- School of Earth, Atmosphere and Environment, Monash University, Clayton, Victoria 3800 Australia
| | - Margaret Byrne
- Science and Conservation Division, Department of Parks and Wildlife, Perth, Western Australia Australia
| | - Stefan Caddy-Retalic
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace Adelaide, South Australia 5005 Australia
| | | | - David J Coates
- Science and Conservation Division, Department of Parks and Wildlife, Perth, Western Australia Australia
| | - Carolina Correa
- Ramaciotti Centre for Genomics, University of New South Wales, Sydney, New South Wales Australia
| | - Belinda C Ferrari
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052 Australia
| | | | - Kelly Hamonts
- CSIRO, National Research Collections Australia, Canberra, Australian Capital Territory Australia ; Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales Australia
| | - Asha Haslem
- Australian Genome Research Facility Ltd, Walter and Eliza Hall Institute, Parkville, Victoria Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072 Australia ; Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072 Australia
| | - Mirko Karan
- Australian SuperSite Network, James Cook University, Townsville, Queensland Australia
| | - Jason Koval
- Ramaciotti Centre for Genomics, University of New South Wales, Sydney, New South Wales Australia
| | - Andrew J Lowe
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace Adelaide, South Australia 5005 Australia
| | | | - Leanne McGrath
- Australian Genome Research Facility Ltd, Adelaide, South Australia Australia
| | - David Martin
- Atlas of Living Australia, CSIRO, Canberra, Australian Capital Territory Australia
| | - Matt Morgan
- CSIRO Land and Water, Canberra, ACT Australia
| | - Kristin I North
- Ramaciotti Centre for Genomics, University of New South Wales, Sydney, New South Wales Australia
| | | | - Elise Pendall
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales Australia
| | - Lori Phillips
- DEDJTR Rutherglen, Melbourne, Victoria Australia ; Agriculture and Agri-food Canada, Science and Technology branch, 2585 County Road 20, Harrow, ON N0R 1G0 Canada
| | - Rebecca Pirzl
- Atlas of Living Australia, CSIRO, Canberra, Australian Capital Territory Australia
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales Australia
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072 Australia
| | - Susanne Schmidt
- School of Agriculture and Food Science, The University of Queensland, St Lucia, Queensland 4072 Australia
| | - Nicole Seymour
- Department of Agriculture and Fisheries, Brisbane, Queensland Australia
| | - Ian Snape
- Australian Antarctic Division, Department of Sustainability, Environment, Water, Population and Communities, 203 Channel Highway, Kingston, Tasmania 7050 Australia
| | - John R Stephen
- Australian Genome Research Facility Ltd, Adelaide, South Australia Australia
| | - Matthew Stevens
- Australian Genome Research Facility Ltd, Walter and Eliza Hall Institute, Parkville, Victoria Australia
| | - Matt Tinning
- Australian Genome Research Facility Ltd, Walter and Eliza Hall Institute, Parkville, Victoria Australia
| | | | - Yun Kit Yeoh
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072 Australia ; Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072 Australia
| | - Carla M Zammit
- University of Queensland, Earth Sciences, St Lucia, Brisbane, Queensland 4072 Australia
| | - Andrew Young
- CSIRO, National Research Collections Australia, Canberra, Australian Capital Territory Australia
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Hayden HL, Mele PM, Bougoure DS, Allan CY, Norng S, Piceno YM, Brodie EL, Desantis TZ, Andersen GL, Williams AL, Hovenden MJ. Changes in the microbial community structure of bacteria, archaea and fungi in response to elevated CO(2) and warming in an Australian native grassland soil. Environ Microbiol 2012; 14:3081-96. [PMID: 23039205 DOI: 10.1111/j.1462-2920.2012.02855.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 07/22/2012] [Indexed: 11/28/2022]
Abstract
The microbial community structure of bacteria, archaea and fungi is described in an Australian native grassland soil after more than 5 years exposure to different atmospheric CO2 concentrations ([CO2]) (ambient, +550 ppm) and temperatures (ambient, + 2°C) under different plant functional types (C3 and C4 grasses) and at two soil depths (0-5 cm and 5-10 cm). Archaeal community diversity was influenced by elevated [CO2], while under warming archaeal 16S rRNA gene copy numbers increased for C4 plant Themeda triandra and decreased for the C3 plant community (P < 0.05). Fungal community diversity resulted in three groups based upon elevated [CO2], elevated [CO2] plus warming and ambient [CO2]. Overall bacterial community diversity was influenced primarily by depth. Specific bacterial taxa changed in richness and relative abundance in response to climate change factors when assessed by a high-resolution 16S rRNA microarray (PhyloChip). Operational taxonomic unit signal intensities increased under elevated [CO2] for both Firmicutes and Bacteroidetes, and increased under warming for Actinobacteria and Alphaproteobacteria. For the interaction of elevated [CO2] and warming there were 103 significant operational taxonomic units (P < 0.01) representing 15 phyla and 30 classes. The majority of these operational taxonomic units increased in abundance for elevated [CO2] plus warming plots, while abundance declined in warmed or elevated [CO2] plots. Bacterial abundance (16S rRNA gene copy number) was significantly different for the interaction of elevated [CO2] and depth (P < 0.05) with decreased abundance under elevated [CO2] at 5-10 cm, and for Firmicutes under elevated [CO2] (P < 0.05). Bacteria, archaea and fungi in soil responded differently to elevated [CO2], warming and their interaction. Taxa identified as significantly climate-responsive could show differing trends in the direction of response ('+' or '-') under elevated CO2 or warming, which could then not be used to predict their interactive effects supporting the need to investigate interactive effects for climate change. The approach of focusing on specific taxonomic groups provides greater potential for understanding complex microbial community changes in ecosystems under climate change.
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Affiliation(s)
- Helen L Hayden
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, 1 Park Drive, Bundoora, Victoria, 3083, Australia.
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