Sugarcane hosts a rich and diverse fungal and bacterial microbiome with the potential to contribute to the crop’s sustainability

Two publications by a consortium of researchers from the GeBioPAD (Genomics and Biotechnology of Plant-Associated Diazotrophs) CBGP group and the University of Campinas (UNICAMP, Brazil) describe the richness and diversity of the microbiome associated to sugarcane using metagenomic and culture-based approaches.

 

Two publications by a consortium of researchers from the GeBioPAD (Genomics and Biotechnology of Plant-Associated Diazotrophs) CBGP group and the University of Campinas (UNICAMP, Brazil) describe the richness and diversity of the microbiome associated to sugarcane using metagenomic and culture-based approaches. This consortium has been organized under the umbrella of the UPM-UNICAMP Joint Centre, with the support of Repsol and Repsol-Sinopec.


Sugarcane is the most photosynthetically efficient crop, with yields that widely exceed 120 Tm biomass per Ha. Brazil is the largest sugarcane and sugar world producer, so much so that part of that sugar is transformed into automotive ethanol, in what represents the most successful biofuel industry to date. Sugarcane cultivation in Brazil is highly sustainable and only modest fertilizer inputs support continued high yields. It has long been suspected that sugarcane relies on associated microorganisms to ensure this sustainability, but until now a comprehensive inventory of the sugarcane microbiome was lacking. Through the use of state-of-the-art NGS methodologies, the existence of a diverse and abundant bacterial (over 23,800 different OTUs) and, notably, fungal (over 11,000 OTUS) microbiome, characteristically distributed all over the different plant compartments has been uncovered. Despite its diversity, the microbiome is dominated by a limited number of core microbial families that harbor traits potentially relevant for plant growth and downstream sugar fermentation processes. In this regard, the high abundance of yeasts as components of the stalk microbiome is noteworthy.


In a companion publication, the construction of a large community-based microbiome collection derived from the sugarcane microbiome is described, as well as a novel high-throughput methodology for near-complete 16S rRNA gene characterization based on multiplexed amplicon sequencing with the PacBio RSII platform, are described. Cross-referencing this information with the previously obtained data on sugarcane microbiome structure and abundance will allow identification of isolates that potentially drive the microbiome structure and function, thus opening the way to design and test synthetic microbiomes with a capacity to enhance plant growth and yield.

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Original Paper:

de Souza, RS; Okura, VK; Armanhi, JS; Jorrin, B; Lozano, N; da Silva, MJ; Gonzalez-Guerrero, M; de Araujo, LM; Verza, NC; Bagheri, HC; Imperial, J; Arruda, P. 2016. "Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome". Scientific Reports. DOI: 10.1038/srep28774".


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