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The microbiome of continuous wheat rotations: minor shifts in bacterial and archaeal communities but a source for functionally active plant-beneficial bacteria

Andrea Braun-Kiewnick, Adriana Giongo, Priscilla M. Zamberlan, Patrick Pluta, Heinz-Josef Koch, Henning Kage, Kornelia Smalla, Doreen Babin

How to cite this work

Braun-Kiewnick A, Giongo A, Zamberlan PM, Pluta P, Koch H-J, Kage H, Smalla K, Babin D (2024) The microbiome of continuous wheat rotations: minor shifts in bacterial and archaeal communities but a source for functionally active plant-beneficial bacteria. Phytobiomes Journal (in press).
DOI: 10.1094/PBIOMES-05-24-0054-R

Data

Unassembled raw amplicon data were deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProjects PRJNA940360 and PRJNA1099798.

Supplementary Material

The Supplementary Material for this article can be found online at:

Abstract

Continuous wheat cropping often leads to yield decline, with suspected causes including increased pathogen susceptibility, decreased root growth, or low nutrient use efficiency, though the exact causes remain unknown. Here, we investigated soil and root-associated communities in wheat under rotation versus continuous cultivation, monitored fungal pathogen presence, and used beneficial bacteria to mitigate Gaeumannomyces tritici (Ggt) symptoms in greenhouse experiments. Sampling was conducted at two field sites with different soil textures over two years and at two plant developmental stages, capturing site-specific and seasonal fluctuations. By cultivation, 767 isolates were screened for plant-beneficial traits. Amplicon sequencing revealed minor effects on community structure due to wheat rotational position but pronounced effects related to site, year, and microhabitat. Rhizoplane isolates with plant-beneficial traits were mainly Flavobacterium, Microbacterium, Pedobacter, Pseudomonas, Stenotrophomonas, and Variovorax. Continuous wheat rotations showed the highest proportion of bacteria with fungal antagonistic potential, indicating plant roots’ recruitment of beneficial bacteria. Introducing Ggt in the greenhouse experiment altered the bacterial and archaeal community, confirming field study results and demonstrating that applying beneficial bacteria early in the season at the seedling stage can control Ggt and improve plant growth. This study highlights the dynamic nature of wheat's below-groundvcommunity, influenced by soil type, season, and microhabitat, with wheat rotation playing a minor role. In addition, it confirms the potential of selected Bacillus and Pseudomonas isolates, whether used individually or in consortia, for microbe- assisted mitigation of yield decline in intensive wheat production.

Funding

This work was conducted within the RhizoWheat Project (www.rhizowheat.uni-kiel.de), project number 031B0910D (Julius Kühn Institute), 031B0910C (Institute of Sugar Beet Research), and 031B0910A (Kiel), funded by the Federal Ministry of Education and Research (BMBF) under the Funding Program Rhizo4Bio. AG was funded through the 2018-2019 BiodivERsA3 ERA-Net COFUND program and with the funding organization DFG (SM 59/21-1).

More info

https://www.rhizowheat.uni-kiel.de/de
https://www.julius-kuehn.de/en/ep

Submission

1. Submitted to Phytobiomes Journal on 22.05.2024.

2. Reviewers comments on 17.06.2024 (deadline 17.09.2024)

• First round to co-authors: 03.07.2024
• Second round to co-authors: 26.07.2024
• Third round to co-authors: 09.08.2024

3. Re-submission to Phytobiomes Journal on 18.08.2024.

4. Accepted at Phytobiomes Journal on 27.08.2024.

• Submission of docx file and high quality figures using WeShare: 30.08.2024
• Submission of First Look: 23.09.2024

5. Online version at Phytobiomes Journal

• First look: 25.09.2024