Molecular Ecological Network Analyses MENA Ye Deng Ph

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Molecular Ecological Network Analyses (MENA) Ye Deng, Ph. D Postdoctoral Research Associate Institute of

Molecular Ecological Network Analyses (MENA) Ye Deng, Ph. D Postdoctoral Research Associate Institute of Environmental Genomics The University of Oklahoma May, 2011 INSTITUTE FOR ENVIRONMENTAL GENOMICS UNIVERSITY OF OKLAHOMA

From parts to interactions Microbial species richness Species diversity Species network intro RMT Species

From parts to interactions Microbial species richness Species diversity Species network intro RMT Species abundance Different species Species interactions analysis Adjacent matrix: Simpson index: concln Shannon index: … Conventional methods: Shannon diversity indexes • • Species number and abundance of each species http: //ieg 2. ou. edu/MENA Ignore interactions among different species

Molecular Ecological network construction intro High throughput sequencing data (e. g. 16 S pyrosequencing)

Molecular Ecological network construction intro High throughput sequencing data (e. g. 16 S pyrosequencing) or Microarray data RMT Standardized relative abundance (SRA) of sequence numbers in a community analysis concln Pair-wise similarity of gene abundance across different samples: e. g. Pearson correlation Determination of adjacency matrix by RMT-based approach http: //ieg 2. ou. edu/MENA

The RMT-based network construction intro RMT analysis concln Luo, Yang et al. BMC Bioinformatics,

The RMT-based network construction intro RMT analysis concln Luo, Yang et al. BMC Bioinformatics, 2007, 8: 299. http: //ieg 2. ou. edu/MENA

The RMT-based network construction intro RMT analysis concln • Each node indicates a OTU

The RMT-based network construction intro RMT analysis concln • Each node indicates a OTU / species and different colors demonstrate the genus they belong to • The edge indicates the interaction between the linkedhttp: //ieg 2. ou. edu/MENA the OTUs/species

The Molecular Ecological Network analyses intro o Overall, what is the network topology? the

The Molecular Ecological Network analyses intro o Overall, what is the network topology? the general network properties and modular structure RMT o For individual species, who are the major players? the important nodes in the system analysis concln o How does the network? the network individuals/modules’ functions o For multiple networks, what are the differences between them? the network comparisons http: //ieg 2. ou. edu/MENA

The steps of MENA intro Network characterization and module detection RMT Identification of topological

The steps of MENA intro Network characterization and module detection RMT Identification of topological roles of individual nodes analysis Eigengene network analyses concln Network comparison between different conditions Association of network properties to ecological functional traits http: //ieg 2. ou. edu/MENA

Responses of grass ecosystems to elevated CO 2 intro RMT Bio. CON (Biodiversity, CO

Responses of grass ecosystems to elevated CO 2 intro RMT Bio. CON (Biodiversity, CO 2, and Nitrogen) at the University of Minnesota by Peter Reich Elevated CO 2 analysis concln Ambient CO 2 Each ring: 20 m diameter There are 296 plots in total. Each plot: 2× 2 m http: //ieg 2. ou. edu/MENA

Modular organization of the MEN under ambient CO 2 intro RMT analysis concln •

Modular organization of the MEN under ambient CO 2 intro RMT analysis concln • • • Based on 454 sequencing data at ambient CO 2. All the MENs examined were modular, with distinct modules. A module is a group of OTUs/functional genes that are highly correlated among themselves, but have few connections with OTUs/functional genes belonging to http: //ieg 2. ou. edu/MENA other modules.

The topological roles of nodes under ambient and elevated CO 2 intro RMT analysis

The topological roles of nodes under ambient and elevated CO 2 intro RMT analysis concln http: //ieg 2. ou. edu/MENA

Effects of e. CO 2 on the network interactions of Actinobacteria intro e. CO

Effects of e. CO 2 on the network interactions of Actinobacteria intro e. CO 2 a. CO 2 RMT analysis concln • • Top 10 OTUs with the highest connectivity at e. CO 2 and their corresponding OTUs at a. CO 2 More complicated network interactions at e. CO 2 than a. CO 2 http: //ieg 2. ou. edu/MENA

Effects of e. CO 2 on the network interactions of Verrucomicrobia intro a. CO

Effects of e. CO 2 on the network interactions of Verrucomicrobia intro a. CO 2 e. CO 2 RMT analysis concln • Oppositely, the interaction of Verrucomircrobia was much less under e. CO 2 than a. CO 2. http: //ieg 2. ou. edu/MENA

Network connectivity vs. the soil geochemical traits intro a. CO 2 Phylogeny Network size

Network connectivity vs. the soil geochemical traits intro a. CO 2 Phylogeny Network size RMT analysis concln e. CO 2 r. M p Network size r. M p All detected OTUs 292 0. 039 0. 169 263 0. 368 0. 001 Acidobacteria 45 0. 054 0. 262 34 0. 137 0. 124 Actinobacteria 81 0. 381 0. 002 76 0. 562 0. 001 Bacteroidetes 23 -0. 084 0. 622 24 0. 487 0. 012 Firmicutes 11 0. 023 0. 338 8 0. 310 0. 114 Gemmatimonadetes 10 -0. 220 0. 958 8 0. 299 0. 168 Planctomycetes 4 0. 604 0. 221 5 -0. 651 1. 000 α-Proteobacteria 45 -0. 034 0. 638 42 0. 472 0. 001 β-Proteobacteria 22 0. 029 0. 319 24 0. 297 0. 044 δ-Proteobacteria 6 0. 498 0. 138 8 0. 043 0. 416 γ-Proteobacteria 11 -0. 159 0. 723 9 0. 020 0. 399 Verrucomicrobia 12 0. 184 0. 057 9 0. 086 0. 253 http: //ieg 2. ou. edu/MENA

Conclusion intro RMT analysis concln o The high-throughput metagenomic data provide a great opportunity

Conclusion intro RMT analysis concln o The high-throughput metagenomic data provide a great opportunity to study the microbial interactions in a large scale o The network analysis can help to identify the key species, compare community structure under different treatments, and link the network topology with environmental traits o Elevated CO 2 dramatically altered the network interactions, indicating the switch of microbial community http: //ieg 2. ou. edu/MENA

Acknowledgement intro RMT analysis concln o o o Jizhong (Joe) Zhou Zhili He Liyou

Acknowledgement intro RMT analysis concln o o o Jizhong (Joe) Zhou Zhili He Liyou Wu Feng Luo Yunfeng Yang Funding Source: o US Department of Energy o United States Department of Agriculture Welcome to our online MENA pipeline: http: //ieg 2. ou. edu/MENA