Microbial Community Analysis in Sediments

The alpha-diversity indices and Bray-Curtis similarities between samples were computed using Primer 6 (Plymouth Marine Laboratory, UK). Jaccard similarity index, bacterial community compositions and relative abundance comparisons were analyzed by R software. One-way analysis of community similarity (ANOSIM) of different layers and non-metric multidimensional scaling (NMDS) were performed in Primer 6. A standard Mantel test at each sampling layer was run in R to evaluate the correlation between horizontal geographic distance and bacterial community compositions (based on the abundances of the top 50 OTUs). Redundancy analysis (RDA) was implemented with Monte Carlo permutation tests to analyze variations in the bacterial assemblages under the constraint of environmental factors by Canoco (Version 5, Microcomputer Power). Significant environmental parameters without multicolinearity effects (variance inflation factor < 20) were obtained to explain community variability^{31 (link)}. BIOENV and BVSTEP analyses were then performed in order to statistically determine correlations between community compositions and environmental variables.

Free full text: Click here

Li Y., Sun L.L., Sun M.L., Su H.N., Zhang X.Y., Xie B.B., Chen X.L., Zhang Y.Z, & Qin Q.L. (2018). Vertical and horizontal biogeographic patterns and major factors affecting bacterial communities in the open South China Sea. Scientific Reports, 8, 8800.

Publication 2018

Canoco

Bacterial Marine Primer

Corresponding Organization :

Other organizations : Shandong University, Qingdao National Laboratory for Marine Science and Technology

Top 5 similar protocols

Variable analysis

independent variables

Horizontal geographic distance

dependent variables

Alpha-diversity indices
Bray-Curtis similarities between samples
Jaccard similarity index
Bacterial community compositions
Relative abundance comparisons

control variables

Sampling layers

controls

Positive controls not explicitly mentioned.
Negative controls not explicitly mentioned.

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!