Soil microbial community responses to different sugarcane management strategies as revealed by 16S metagenomics

CECILIA A. FONTANA; SERGIO M. SALAZAR; LUGI ORRU; GRACIELA M. VIGNOLO; PAOLA D. FONTANA; PIER S. COCCONCELLI

Tucuman

Congreso; XXX Congreso International de la Caña de Azucar; 2019

International Society of Sugar Cane Technologists

Sugarcane cultivation in Argentina is distributed in three geographic regions: Tucumán, Northern (Salta and Jujuy) and Littoral (Santa Fe and Misiones), covering about 376,223 ha. Tucumán has traditionally been the most important region with 68% of the total production. Since new agricultural techniques, such as green-cane harvesting and sugarcane crop rotation with soybean, were implemented in the last decade, changes in the agroecosystem of sugarcane, specific pathosystems and epidemiological parameters have been observed. A 16S metagenomics approach to investigate total bacterial communities associated with sugarcane rhizospheric soil when soybean was the predecessor crop in a cultivation area with a high incidence of red stripe disease was applied; soil from sugarcane monoculture was also included. Two commercial sugarcane cultivars (Saccharum spp. hybrids) with differential responses to red stripe infection (tolerant and susceptible) were evaluated. Sampling was carried out in 2013-2014 and in 2014-2015 (first and second ratoon, respectively) at 30, 90 and 180 days after harvest. Total soil DNA was obtained using FastPrep® technology. The 16S RNA gene (variable region V3-V4) was sequenced using a MiSeq platform Illumina. Taxonomic assignment revealed Bacillales, Rhyzobiales, Rhodospirilliales, Xanthomonadales and Acidobacteriales among the most abundant orders in all samples. Soil samples from sugarcane without soybean rotation showed a marked decrease in Bacillaes, Rhizobiales and Sphingomonadales. Cluster analysis grouped together samples from the tolerant genotype, while those from the susceptible genotype formed two subgroups that were distinguished according to sampling time after harvest. The analysis showed that samples from sugarcane under monoculture were grouped distant to the rest of the samples showing different microbiota composition. The sugarcane rhizosphere microbiome and its biotechnological potential open a new opportunity in the concept of sustainable crop management. The data contribute significant knowledge about the microbial diversity in agricultural ecosystems.