Bacterial communities estimated by pyrosequencing in the soils of chinampa, a traditional sustainable agro-ecosystem in Mexico

As artificial islands created by accumulation of sediments and litters, chinampas formed a unique and sustainable agro-ecosystem. However, no investigation on the chinampa microbial communities has been reported. With the goal of revealing the soil bacterial communities in the chinampas and their changes influenced by environmental conditions, soils were sampled for determining their bacterial communities. Soil samples were collected from a cultivated and an abandoned chinampa at two horizontal layers and from rhizosphere of Portulaca oleracea L. The bacterial community composition was assayed by 454 high-throughput pyrosequencing. The correlation between environmental parameters and bacterial diversity was analyzed. Sequence analysis based on the V1-V3 regions of 16S rRNA gene obtained 140,790 bacterial tags. A total of 22 phyla and 30 candidate divisions were detected in the chinampa soils. The dominant phyla were Proteobacteria, Chloroflexi, Firmicutes, Bacteroidetes, and Acidobacteria. Bacillus, Thiobacillus, Nitrospira, and Planctomyces were the principal genera. Greater bacterial diversity was revealed in the superficial soils than in the deep-layer soils and in bulk soils than in the rhizosphere. The structure of microbial communities in the rhizosphere was remarkably different from that of communities in the bulk soils. Canonical correspondence analysis (CCA) revealed that contents of nitrogen were negatively correlated with Chlorobi, Verrucomicrobia, Gemmatimonadetes, and Acidobacteria but favored Cyanobacteria, Bacteroidetes, and Nitrospirae, whereas total organic carbon and electrical conductivity were positively correlated with Actinobacteria and Chloroflexi. As the first exhaustive census on the bacterial communities in chinampa soils, our study demonstrates that the chinampas harbor diverse bacteria from soil and sediments and the agricultural activity and rhizosphere effect can shape the microbial communities in this singular agro-ecosystem.