Microbial community composition of the Danshui river estuary of Northern Taiwan and the practicality of the phylogenetic method in microbial barcoding.
In this study, the microbial community in a mangrove ecosystem was surveyed and used to test the eligibility of 16S rDNA library and neighbor-joining method for the purpose of estimating microbial composition. Genetic diversity (pi) and four other diversity indices (Simpson's unbiased, Shannon-Wiener, Evenness, and Chao1 indices) were applied to estimate the adaptive lineages of microorganisms in the mangrove ecosystem. The results indicated that gamma-Proteobacteria is the most diverse taxon, while the most abundant family is Rhodobacteraceae (alpha-Proteobacteria), followed by Comamonadaceae (beta-Proteobacteria). This result may imply the existence of a graded distribution of microbial diversity across a spectrum of different salinities in the waterbody of this estuary ecosystem. Furthermore, at least 500-1,000 bps of the posterior portion of 16S rDNA is required as a marker to profile the microbial diversity in a microcosm of interest using phylogenetic methods, according to the results of our sliding window analyses for the measurements of pi, consistency index, and retention index.
Liao
Pei-Chun
PC
Department of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sect. 4, Taipei, 116, Taiwan, Republic of China.
Huang
Bing-Hong
BH
Huang
Shong
S
D044822:Biodiversity; D042621:Comamonadaceae / Q000145:classification / Q000235:genetics; D017753:Ecosystem; D020563:Gammaproteobacteria / Q000145:classification / Q000235:genetics; D014644:Genetic Variation; D005843:Geography; D008969:Molecular Sequence Data; D010802:Phylogeny; D020560:Proteobacteria / Q000145:classification / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D041902:Rhodobacteraceae / Q000145:classification / Q000235:genetics; D045483:Rivers / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D013624:Taiwan; D014871:Water Microbiology
D012336:RNA, Ribosomal, 16S