Bacterial community structure and diversity of two closely located stations are usually considered similar which can be verified by more intensive investigations using relatively large amount of datasets from the next...Bacterial community structure and diversity of two closely located stations are usually considered similar which can be verified by more intensive investigations using relatively large amount of datasets from the next generation sequencer. This study was conducted to assess the bacterial community structure and diversity between two closely located coastal stations, the port side and the sea side of the Oarai, Ibaraki, Japan from March 2013 to July 2014 using 454 GS Junior sequencer. Two stations underwent similar changes in physicochemical properties but the community structure and diversity was different. The Proteobacteria (the class Alphaproteobacteria, followed by the Gammaproteobacteria) and the Bacteroidetes (the class Flavobacteriia) were two abundant phyla in both the stations. But, the Flavobacteriia was more abundant in the port side, contributed about 26% to 48%, compared to the sea side (about 12% to 39%). Conversely, the relative abundance of the Gammaproteobacteria was higher on the sea side, about 10% to 17%, compared to the port side (about 4% to 12%). Among others, the phyla Cyanobacteria, Deferribacteres, Verrucomicrobia and the class Betaproteobacteria were also relatively abundant at the sea side. Because of their dominancy, the class Flavobacteriia and Alphaproteobacteria were further analysed at a lower phylogenetic level and marked differences were observed between the stations. Bacterial biodiversity in terms of the species richness (Chao index) and evenness (inverse Simpson) indicated higher patterns of diversity in the sea side area compared to the port side. Non-metric Multidimensional Scaling fitting with the environmental features (metaMDS), redundancy analysis (RDA) and Bray-Curtis clustering analysis also showed marked differences in bacterial community structure and diversity between the stations. However, some OTUs were commonly found in both the stations in all the sampling periods. So, the bacterial community structure and diversity of the coastal areas are distinguishable even between two closely located sampling points.展开更多
A number of basic and applied questions in ecology and environmental management require the characterization of soil and leaf litter faunal diversity. Recent advances in high-throughput sequencing of barcode-gene ampl...A number of basic and applied questions in ecology and environmental management require the characterization of soil and leaf litter faunal diversity. Recent advances in high-throughput sequencing of barcode-gene amplicons ('metabarcoding') have made it possible to survey biodiversity in a robust and efficient way. However, one obstacle to the widespread adoption of this technique is the need to choose amongst many candidates for bioinformatic processing of the raw sequencing data. We compare three candidate pipelines for the processing of 18S small subunit rDNA metabarcode data from solid substrates: (i) USEARCH/CROP, (ii) Denoiser/UCLUST, and (iii) OCTUPUS. The three pipelines produced reassuringly similar and highly correlated assessments of community composition that are dominated by taxa known to characterize the sampled environments. However, OCTUPUS appears to inflate phylogenetic diversity, because of higher sequence noise. We therefore recommend either the USEARCH/CROP or Denoiser/UCLUST pipelines, both of which can be run within the QIIME (Quantitative Insights Into Microbial Ecology) environment.展开更多
文摘Bacterial community structure and diversity of two closely located stations are usually considered similar which can be verified by more intensive investigations using relatively large amount of datasets from the next generation sequencer. This study was conducted to assess the bacterial community structure and diversity between two closely located coastal stations, the port side and the sea side of the Oarai, Ibaraki, Japan from March 2013 to July 2014 using 454 GS Junior sequencer. Two stations underwent similar changes in physicochemical properties but the community structure and diversity was different. The Proteobacteria (the class Alphaproteobacteria, followed by the Gammaproteobacteria) and the Bacteroidetes (the class Flavobacteriia) were two abundant phyla in both the stations. But, the Flavobacteriia was more abundant in the port side, contributed about 26% to 48%, compared to the sea side (about 12% to 39%). Conversely, the relative abundance of the Gammaproteobacteria was higher on the sea side, about 10% to 17%, compared to the port side (about 4% to 12%). Among others, the phyla Cyanobacteria, Deferribacteres, Verrucomicrobia and the class Betaproteobacteria were also relatively abundant at the sea side. Because of their dominancy, the class Flavobacteriia and Alphaproteobacteria were further analysed at a lower phylogenetic level and marked differences were observed between the stations. Bacterial biodiversity in terms of the species richness (Chao index) and evenness (inverse Simpson) indicated higher patterns of diversity in the sea side area compared to the port side. Non-metric Multidimensional Scaling fitting with the environmental features (metaMDS), redundancy analysis (RDA) and Bray-Curtis clustering analysis also showed marked differences in bacterial community structure and diversity between the stations. However, some OTUs were commonly found in both the stations in all the sampling periods. So, the bacterial community structure and diversity of the coastal areas are distinguishable even between two closely located sampling points.
基金supported by Yunnan Province (20080A001)Chinese Academy of Sciences (0902281081,KSCX2-YW-Z-1027)+2 种基金the National Natural Science Foundation of China (31170498)Ministry of Science and Technology of China (2012FY110800)Kunming Institute of Zoology,and the University of East Anglia
文摘A number of basic and applied questions in ecology and environmental management require the characterization of soil and leaf litter faunal diversity. Recent advances in high-throughput sequencing of barcode-gene amplicons ('metabarcoding') have made it possible to survey biodiversity in a robust and efficient way. However, one obstacle to the widespread adoption of this technique is the need to choose amongst many candidates for bioinformatic processing of the raw sequencing data. We compare three candidate pipelines for the processing of 18S small subunit rDNA metabarcode data from solid substrates: (i) USEARCH/CROP, (ii) Denoiser/UCLUST, and (iii) OCTUPUS. The three pipelines produced reassuringly similar and highly correlated assessments of community composition that are dominated by taxa known to characterize the sampled environments. However, OCTUPUS appears to inflate phylogenetic diversity, because of higher sequence noise. We therefore recommend either the USEARCH/CROP or Denoiser/UCLUST pipelines, both of which can be run within the QIIME (Quantitative Insights Into Microbial Ecology) environment.
