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Roots of Decline
This document summarizes a research project studying the assembly and function of the rhizosphere microbiome in relation to declining oilseed rape yields. The project has multiple work packages investigating how the microbiome is assembled based on rotation, environment and geography. It will analyze microbiome composition and function under different rotation frequencies and soil management practices. The goal is to understand what determines a "good" versus "bad" microbiome and how to engineer one that improves yields. The research involves field sites, DNA sequencing, metatranscriptomics and experiments with contrasting crop varieties and soil amendments.
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Roots of Decline
- 1. Gary Bending School ofLife Sciences, University of Warwick, UK Roots of decline? Assembly and function of the rhizosphere microbiome in relation to yield decline
- 2. Penny Hirsch Tim Mauchline IanClark Peter Mills Grace Smith Chris van der Gast Anna Oliver David Bass Keith Norman Sam Maycock Gary Bending Graham Teakle Jay Moore Project Partners
- 3. Penny Hirsch Tim Mauchline IanClark Susanne Schreiter (PDRA) Peter Mills Grace Smith Chris van der Gast Anna Oliver David Bass Keith Norman Sam Maycock Gary Bending Graham Teakle Jay Moore Sally Hilton (PDRA) Sarah Thornber (RA) Project Team
- 4. OSR yield declineswith increased frequency in rotations £43-86 million annual loss http://cereals.ahdb.org.uk/media/305093/g55-oilseed-rape-guide- jan-2014-update.pdf Bennett et al. 2012 Biol. Rev. 87, 52–71
- 5. OSR yield declineswith increased frequency in rotations £43-86 million annual loss http://cereals.ahdb.org.uk/media/305093/g55-oilseed-rape-guide- jan-2014-update.pdf
- 6. OSR yield declineswith increased frequency in rotations £43-86 million annual loss http://cereals.ahdb.org.uk/media/305093/g55-oilseed-rape-guide- jan-2014-update.pdf What determines assembly of the rhizosphere microbiome? What do ‘good’ and ‘bad’ microbiomes look like? How do good and bad microbiomes interact with the plant? Can we engineer a ‘good’ microbiome?
- 7. WP 1 Whatcontrols assembly of the rhizosphere microbiome at the landscape scale? • Multiple microbial taxa • Rotation, environment, geography
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- 12. Sampling strategy = 5root, 5 rhizosphere and 5 bulk soil samples for DNA = 15 samples/site x 37sites =555 samples
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- 18. Vortex Vortex InvertInvert Pool and spin 25 ml sterile water Processing procedure Bulk soil Root/Rhizoplane Rhizosphere
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- 21. Rotation lengths 0 2 4 6 8 10 12 14 1 in2 1 in 3 1 in 4 1 in 5 1 in 6 1 in 7 1 in 8 1 in 9 1 in 12 Virgin Rotation (frequency of OSR) Numberofsites
- 22. Soil types selectedfor sampling (as defined by land managers) 11 7 6 4 2 1 1 1 1 1 Loam Clay Sandy Clay Loam Brash Clay Loam Chalk River Gravel Silt Silty clay loam Sandy
- 23. Clay Loam, 17 Clay, 11 SiltyClay Loam, 4 Sandy Loam, 3 Sandy Clay Loam, 1 Silty Clay, 1 Sandy loam, 3 Actual soil types sampled Textural Class Sand 2.00- 0.063m m Silt 0.063- 0.002mm Clay <0.002mm F1 Clay Loam 48 31 21 F2 Clay 35 25 40 F3 Clay Loam 32 35 33 F3A Clay Loam 34 35 31 F4 Silty Clay Loam 16 54 30 F5 Clay 14 44 42 5C Clay 23 41 36 F5D Clay Loam 24 48 28 F6 Clay Loam 25 46 29 F7 Sandy Clay Loam 54 22 24 F8A Clay 35 25 40 F8B Clay Loam 28 38 34 F9 Clay Loam 25 42 33 F9A Silty Clay Loam 20 49 31 F10 Clay Loam 32 37 31 F10A Clay Loam 49 31 20 F11 Clay Loam 23 44 33 F12 Clay Loam 32 42 26 F13 Silty Clay Loam 20 46 34 F14A Clay Loam 33 36 31 F14C Clay 24 40 36 F15 Sandy Loam 55 27 18 F15A Clay 26 35 39 F16 Clay Loam 32 44 24 F16A Clay 24 27 49 F17 Clay 19 41 40 F18 Silty Clay Loam 19 48 33 F18A Silty Clay 16 48 36 F19 Clay 22 34 44 F20 Sandy Loam 78 12 10 F21 Clay Loam 38 32 30 F21A Clay 24 33 43 F21B Clay Loam 33 34 33 F21C Clay Loam 31 41 28 F22 Clay 23 40 37 F24 Sandy Loam 65 19 16 F25 Clay Loam 42 30 28
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- 29. Wheat, 18Barley, 13 Fallow,3 Rye, 1 Previous crop
- 30. Sowing date %sitessown 0 20 40 60 80 100 7/30/2014 8/4/20148/9/2014 8/14/2014 8/19/2014 8/24/2014 8/29/2014 9/3/2014 9/8/2014 9/13/2014
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- 32. Amplicon sequencing • 2x300bp MiSeq analysis • Bacterial, fungal and microbial eukaryote communities Follow up with further specific taxa • Which DNA extraction kit to use? FastDNA™ SPIN Kit for Soil (MP Biomedicals)? PowerSoil® DNA Isolation Kit (MO-BIO)?
- 33. Root 0 20 40 60 80 100 120 NR PR WRNRh PRh WRh NS PS WS No wash No wash 0.5 g µg/mlDNA(100ul volume) MoBio 0 20 40 60 80 100 120 NR PR WR NRh PRhWRh NS PS WS µg/ml(totalvolume 100µl) FastDNA Rhizosphere Bulk soil 0 20 40 60 80 100 120 NR PR WR NRh PRh WRh NS PS WS Griffiths Root Rhizosphere Bulk soil Root Rhizosphere Bulk soil DNA extraction
- 34. ITS CEH 33K Resemblance:S17 Bray Curtis similarity KitSoil type2 FP1 FP2 FP3 MB1 MB2 MB3 2D Stress: 0.01 ITS 0 100 200 300 400 1 2 3 FP MB No.OTUs Soil type
- 35. WP2 Functional responsesof the rhizosphere microbiome to rotation • Different rotation frequencies of OSR • Trials at Warwick Crop Centre, Harper-Adams and Rothamsted • Metatranscriptome analysis • Cross-talk between plant roots and microbial community • Pathways associated with host defence, nutrient uptake and assimilation
- 36. WP 2 Structureand function of the microbiome Rotation 2014-15 2015-16 2016-17 2017-18 Continuous OSR Wheat OSR OSR OSR Alternate OSR Wheat OSR Wheat OSR Virgin OSR Wheat Wheat Wheat OSR Rotation 2013-14 2014-15 2015-16 2016-17
- 37. Rothamsted White horse plot2 – 4/6/2015
- 38. Rothamsted Scout plot 2– 4/6/2015
- 39. WP3 Rhizosphere engineeringvia crop genotype • Contrasting varieties grown in rotation • Microbiome assembly • Metatranscriptome profiling 2 x 6 m plots
- 40. WP4 Rhizosphere engineeringvia soil management • Furzefield site at Rothamsted • Cropped continuously with OSR since 1991 • Yields have declined by 30 % Rotation 2013-2014 2014-2015 2015-2016 1. Continuous OSR OSR OSR OSR 2. FYM OSR FYM/OSR OSR 3. Biosolids OSR Biosolids/OSR OSR 4. Fallow OSR Fallow OSR 5. Legume break OSR Faba beans OSR 6. Oat break OSR Oats OSR 7. Wheat break OSR Wheat OSR
- 41. Impact activities Steering group PaulGosling/ Amanda Bennett, HGCA Andrew Richards, Agrii Mark Nightingale, Elsoms Peter Scott, Origin fertilisers Richard Elsdon, United Oilseeds First meeting 17th November 2015 (Warwick)
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