Evolution of bacterial communities in the wheat crop rhizosphere
Summary The gap between current average global wheat yields and that achievable through best agronomic management and crop genetics is large. This is notable in intensive wheat rotations which are widely used. Expectations are that this gap can be reduced by manipulating soil processes, especially t...
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| Published in | Environmental microbiology Vol. 17; no. 3; pp. 610 - 621 |
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| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Blackwell Publishing Ltd
01.03.2015
Wiley Subscription Services, Inc |
| Subjects | |
| Online Access | Get full text |
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| Summary: | Summary
The gap between current average global wheat yields and that achievable through best agronomic management and crop genetics is large. This is notable in intensive wheat rotations which are widely used. Expectations are that this gap can be reduced by manipulating soil processes, especially those that involve microbial ecology. Cross‐year analysis of the soil microbiome in an intensive wheat cropping system revealed that rhizosphere bacteria changed much more than the bulk soil community. Dominant factors influencing populations included binding to roots, plant age, site and planting sequence. We demonstrated evolution of bacterial communities within the field rhizosphere. Early in the season, communities tightly bound to the root were simplest. These increased in diversity with plant age and senescence. Loosely bound communities also increased in diversity from vegetative to reproductive plant stages but were more stable than those tightly bound to roots. Planting sequence and, to a lesser extent, wheat genotype also significantly affected rhizosphere bacteria. Plasticity in the rhizosphere generated from crop root system management and genetics offers promise for manipulating the soil ecology of intense cereal systems. Analyses of soil microbiomes for the purpose of developing agronomic benefit should include roots as well as soil loosely adhered to the roots, and the bulk soil. |
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| Bibliography: | ark:/67375/WNG-7C0M4WHF-N CSIRO Office of the Chief Executive (OCE) Fig. S1. Field plan and sampling schedule. A. Field plan of experiment on site 1. First year treatments (Janz, H45, fallow soil) were replicated four times in a randomized block design, with composite samples taken from across the whole plot. First year treatments were oversown with Janz (J) and H45 (H) in the second year, and samples taken from subplots marked asterisk. The entire experiment was replicated in the first year on site 2. In the second year the two eastern blocks were unavailable for sampling on site 2 and all subplots in the western blocks were sampled in a pseudoreplicate structure (the total number of samples was the same but taken from only two blocks). B. Sampling schedule. Above the time line are sampling dates with plant stage for samples collected for culturing and T-RFLP, communities from underlined plant stages were also sequenced. Fig. S2. Abundance of cultured populations (log10 transformed) per gram dry weight of LB soil, over 2 years wheat cropping. Each point represents a mean of four samples. Fig. S3. Year 2 vegetative (V2) stage T-RFLP data for A-C: LB and D-F: TB. A and D show principal coordinates analysis of Bray-Curtis similarities for communities labelled by site. Canonical analyses of principal coordinates for a priori groups defined by rotation and genotype are shown within site 1 (B and E) and site 2 (C and F). Colour highlights the genotype sown in the current year (Year 2). Fig. S4. Year 2 reproductive (R2) stage T-RFLP data for A-C: LB and D-F: TB. A and D show principal coordinates analysis of Bray-Curtis similarities for communities labelled by site. Canonical analyses of principal coordinates for a priori groups defined by rotation and genotype are shown within site 1 (B and E) and site 2 (C and F). Note colour highlights the treatment (fallow or wheat genotype) of the previous year (Year 1). Fig. S5. Evolution of bacterial diversity from 454 sequence data. Heatmap with rows showing operational taxonomic units (OTUs) represented by at least three sequences in three samples. Data are log2 transformed. OTUs were defined by 97% sequence similarity. V2W indicates wheat grown after wheat, V2F indicates wheat grown after fallow. Fig. S6. Sequence data allocated to genus level were log (x + 1) transformed, clustered by Bray-Curtis similarity and displayed in multi-dimensional scaling plot. Points representing bacterial communities tightly bound to the root are coloured red and loosely bound communities blue. Plant stages are represented by symbols vegetative: squares, reproductive: triangles and senescing roots: circles. Table S1. Fold changes in genera representing more than 0.5% of the population in any sample. Part A shows a summary of the number of genera changing in pairwise comparisons between i. plant stages within the TB fraction (year 1 vegetative, V1, to year 1 reproductive, R1, to senescing roots, Sb, to year 2 vegetative, V2); and from V1 to V2; ii. plant stages within the LB fraction; iii. TB and LB at each plant stage where both were sequenced from; iv. wheat following fallow, WOF, and wheat following wheat, WOW, within TB and LB soil fractions at V2. Part B lists the genera for each pairwise comparison in the summary table. Appendix S1. Materials and methods. Australian Grains Research and Development Corporation (GRDC) - No. CSP00115 istex:B5A4C903CC4692375CE0962DF2A8BA96282ECAA3 ArticleID:EMI12452 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 |
| ISSN: | 1462-2912 1462-2920 1462-2920 |
| DOI: | 10.1111/1462-2920.12452 |