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Pathobiomes Revealed that Pseudomonas fuscovaginae and Sarocladium oryzae Are Independently Associated with Rice Sheath Rot

Microbial Ecology volume 80, pages 627–642 (2020)Cite this article

Abstract

Rice sheath rot has been mainly associated with the bacterial pathogen Pseudomonas fuscovaginae and in some cases to the fungal pathogen Sarocladium oryzae; it is yet unclear if they are part of a complex disease. The bacterial and fungal community associated with rice sheath rot symptomatic and asymptomatic rice plants was determined/studied with the main aim to shed light on the pathogen(s) causing rice sheath rot. Plant samples were collected from different rice varieties in two locations (highland and lowland) in two rice-growing seasons (wet and dry season) in Burundi. Our results showed that the bacterial Pseudomonas genus was prevalent in highland in both rice-growing seasons and was not affected by rice plant varieties. Pseudomonas sequence reads displayed a significant high similarity to Pseudomonas fuscovaginae indicating that it is the causal agent of rice sheath rot as previously reported. The fungal Sarocladium genus was on the other hand prevalent in lowland only in the wet season; the sequence reads were most significantly similar to Sarocladium oryzae. These studies showed that plant microbiome analysis is very useful in determining the microorganisms involved in a plant disease. P. fuscovaginae and S. oryzae were prevalent in symptomatic samples in highland and lowland respectively being present independently and hence are not part of a complex disease. The significant presence of other bacterial and fungal taxa in symptomatic samples is also discussed possibly making this disease more complex. Finally, we also report the microbial communities that are associated with the plant sheath in symptomatic and asymptomatic plants from the same rice fields.

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Abbreviations

OTU:

operational taxonomic unit

ITS:

internal transcribed spacer

PCR:

polymerase chain reaction

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Acknowledgements

We acknowledge IRRI-Burundi for laboratory financial support and providing the plant samples used in this work.

Funding

SM was supported by an ICGEB Arturo Falaschi fellowship. This work financially supported by ICGEB and in part by the grant from the Italian MAE-CI (PGR00816/PGR00927/PGR00739).

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Affiliations

  1. International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149, Trieste, Italy

    Samson Musonerimana, Cristina Bez & Vittorio Venturi

  2. ARGO Open Lab Platform for Genome sequencing, AREA Science Park, Padriciano 99, 34149, Trieste, Italy

    Danilo Licastro

  3. International Rice Research Institute (IRRI)-Africa Regional Crop Improvement Office, Burundi University-Faculty of Agronomy and Bio-Engineering, Avenue de l’UNESCO No 2, Bujumbura, Burundi

    Georges Habarugira & Joseph Bigirimana

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  1. Samson Musonerimana
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  2. Cristina Bez
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  3. Danilo Licastro
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Contributions

SM, JB and VV designed the experiments. SM, GH and DL performed the experiments. GH drew and adapted the rice field sites and outstation map of IRRI-Burundi. SM, DL and CB analyzed the data. MS, CB and VV drafted the manuscript. All the authors read and approved the final manuscript.

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Correspondence to Vittorio Venturi.

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Musonerimana, S., Bez, C., Licastro, D. et al. Pathobiomes Revealed that Pseudomonas fuscovaginae and Sarocladium oryzae Are Independently Associated with Rice Sheath Rot. Microb Ecol 80, 627–642 (2020). https://doi.org/10.1007/s00248-020-01529-2

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Keywords

  • Pathobiome
  • Rice sheath rot
  • Pseudomonas
  • Sarocladium
  • Phyllospheric microbiome of rice