Bacterial community variations in an alfalfa-rice rotation system revealed by 16S rRNA gene 454-pyrosequencing

• Published in: FEMS microbiology ecology 2014-03, Vol.87 (3), p.650-663
• Main Authors: Lopes, Ana R., Manaia, Célia M., Nunes, Olga C.
• Format: Article
• Language: English
• Subjects: 454‐pyrosequencing; Aerobic bacteria; Agricultural practices; Agriculture - methods; Alfalfa; Bacteria - classification; Bacteria - genetics; bacterial community; Biodiversity; Cereal crops; Community composition; Crop production; Crop rotation; Crops, Agricultural - growth & development; diversity; DNA Barcoding, Taxonomic; DNA, Bacterial - genetics; Ecology; Harvesting; Medicago sativa - growth & development; Microbial activity; Microbiology; Oryza - growth & development; PCoA; Phylogeny; Relative abundance; Rice; Rice fields; rice paddy soil; RNA, Ribosomal, 16S - genetics; Sequence Analysis, DNA; Soil - chemistry; Soil Microbiology; Sustainable production
• ISSN: 0168-6496; 1574-6941
• DOI: 10.1111/1574-6941.12253

Abstract Crop rotation is a practice harmonized with the sustainable rice production. Nevertheless, the implications of this empirical practice are not well characterized, mainly in relation to the bacterial community composition and structure. In this study, the bacterial communities of two adjacent paddy fields in the 3rd and 4th year of the crop rotation cycle and of a nonseeded subplot were characterized before rice seeding and after harvesting, using 454-pyrosequencing of the 16S rRNA gene. Although the phyla Acidobacteria,Proteobacteria,Chloroflexi,Actinobacteria and Bacteroidetes predominated in all the samples, there were variations in relative abundance of these groups. Samples from the 3rd and 4th years of the crop rotation differed on the higher abundance of groups of presumable aerobic bacteria and of presumable anaerobic and acidobacterial groups, respectively. Members of the phylum Nitrospira were more abundant after rice harvest than in the previously sampled period. Rice cropping was positively correlated with the abundance of members of the orders Acidobacteriales and ‘Solibacterales’ and negatively with lineages such as Chloroflexi ‘Ellin6529’. Studies like this contribute to understand variations occurring in the microbial communities in soils under sustainable rice production, based on real-world data. Variations on the structure and composition of the bacterial communities were related with presence of rice, the phase of the rice cycle production and the stage of crop rotation.