Bacterial phylogenetic diversity in a Spartina marsh in China

Abstract

The bacterial phylogenetic diversities of the bacterial communities in the salt marsh colonized by Spartina alterniflora (SA) and uncultured marsh (UM) along the Yellow Sea of China were analyzed based on the 16S rDNA PCR techniques. Two libraries containing 251 clones of 16S rRNA genes from the Spartina colonized marsh and 283 from UM were constructed by PCR using a bacteria-specific primer 8f and the common primer 1542r. Forty-seven clones from SA and 55 from UM were selected for partial sequencing. A phylogenetic tree was constructed by the alignment analysis of the total environmental DNA sequences. Clones were clustered into 8 divisions of bacteria: (1) Proteobacteria containing 12 genera in beta, gamma, delta and epsilon subdivision; (2) Bacteroidetes containing 7 genera; (3) Planctomycetes containing 2 genera; (4) Firmicutes containing 1 genus; (5) Spirochaetes containing 1 genus; (6) Acidobacteria containing 1 genus; (7) Actinobacteria containing 1 genus; and (8) BRC1 containing 1 genus, as well as 3 groups of bacteria that could not be clustered into any recognized bacterial divisions or candidate divisions. BLAST searches of the GenBank database confirmed that 79.7% of the clones in the two libraries were closely related to the 16S rDNA sequences of the uncultured bacteria with the similarity ≥90%. Among them, Proteobacteria (36.7% and 54.4% of the total clones from the SA and UM libraries, respectively) and Bacteroidetes (30.0% and 18.3%, respectively) are two dominant groups in both the sites. However, some phyla, such as Firmicutes and Actinobacteria, were found at SA site but not at UM site, and vice versa, some phyla, such as Spirochaetes and BRC1, were found at UM, but not at SA. Moreover, the dominant species in each phylum were varied, dependent on whether or not the marsh was colonized by Spartina. For instance, in Bacteroidete, 44.4% clones at SA library were affiliated to Gelidibacter, but 32.7% clones were affiliated to Flexibacter at UM library. In Proteobacteria, the clones at UM library affiliated to δ, γ, ɛ and β-subdivisions were 38.8%, 34.7%, 23.5% and 3.1%, respectively, but at SA library were 30.3%, 47.0%, 13.6% and 9.1%, correspondingly. These results indicated that the bacterial diversity in the salt marsh along the Yellow Sea of China was greatly changed after Spartina colonization.