Using Mothur to Evaluate Bacterial Diversity in Rice Sediments.

Rice paddy fields are characterized by floodwater covering the field surface during the period of rice cultivation.  In the rice field floodwater, the mineralization of crop residues, plant exudates, along with agrochemical inputs and agricultural practices play an important role in microbial community composition. During the development cycle, plants absorb and release ions differently, which can also influence bacterial colonization of plant roots.  This study aims to monitor the bacterial community structure in a rice paddy field in vegetative and reproductive phenological stages.  The field experiment was performed in a paddy fields located in the south of Brazil. Water samples were collected in triplicate from the top 5 cm of the surface plots of rice fields in the vegetative and reproductive rice culture stages, in the agricultural cycles of 2011/12 and 2012/13.  DNA of six replicates from vegetative and reproductive rice growing stages were pooled in equal amounts. These pools were used as template for 16S pyrosequencing analyses. The overall raw data obtained were processed using Mothur. After filtering, pre-clustering and chimera removal the unique sequences were aligned against the SILVA reference database. The high-quality reads were classified (classify.seqs), using the Silva taxonomy. Sequences were categorized into OTUs (operational taxonomic units) at 97% similarity. The heatmaps were built based on the class, phylum, order and family bacterial profile using heatmap.2 R command. Venn diagrams were prepared from the shared OTU table. Bacterial communities from the vegetative rice culture stages were distinct from those of the reproductive rice stages.  Future studies will assess dynamics of microbial community structure in relation to environmental characteristics and physical-chemical water inputs of rice fields.