Molecular ecological network analyses
- Ye Deng, Yi-Huei Jiang, Yunfeng Yang, Zhili He, Feng Luo, Jizhong Zhou
- BiologyBMC Bioinformatics
- 30 May 2012
A novel mathematical and bioinformatics framework to construct ecological association networks named molecular ecological networks (MENs) through Random Matrix Theory (RMT)-based methods is described, which provides powerful tools to elucidate network interactions in microbial communities and their responses to environmental changes.
Stochastic Community Assembly: Does It Matter in Microbial Ecology?
Both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift are described.
Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria
It is reported that the dispersed hydrocarbon plume stimulated deep-sea indigenous γ-Proteobacteria that are closely related to known petroleum degraders, and the potential exists for intrinsic bioremediation of the oil plume in the deep-water column without substantial oxygen drawdown.
A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights
A comprehensive genomic survey indicated that the POCP can serve as a robust genomic index for establishing the genus boundary for prokaryotic groups and integration of whole-genome data into the current taxonomy system can provide comprehensive information.
Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation
- Yongqing Liu, Jizhong Zhou, M. Daly
- BiologyProceedings of the National Academy of Sciences…
- 21 March 2003
Microarray data suggest that DEIRA cells efficiently coordinate their recovery by a complex network, within which both DNA repair and metabolic functions play critical roles, including a predicted distinct ATP-dependent DNA ligase and metabolic pathway switching that could prevent additional genomic damage elicited by metabolism-induced free radicals.
Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2
A novel random matrix theory (RMT)-based conceptual framework is described to discern phylogenetic molecular ecological networks of microbial communities based on high-throughput metagenomic sequencing data, among the first to document that the network interactions among different phylogenetic populations in soil microbial communities were substantially changed by a global change such as an elevated CO2 level.
GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes
This is the first comprehensive microarray currently available for studying biogeochemical processes and functional activities of microbial communities important to human health, agriculture, energy, global climate change, ecosystem management, and environmental cleanup and restoration.
Simultaneous Recovery of RNA and DNA from Soils and Sediments
A robust, simple, rapid, and effective method was developed for simultaneous recovery of both RNA and DNA from soils of diverse composition by adapting the previous grinding-based cell lysis method for DNA extraction.
Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill
The draft genome included genes for chemotaxis, motility and nutrient acquisition strategies that were also identified in the metagenomes and metatranscriptomes, which point towards a rapid response of members of the Oceanospirillales to aliphatic hydrocarbons in the deep sea.
Nitrite Reductase Genes (nirK andnirS) as Functional Markers To Investigate Diversity of Denitrifying Bacteria in Pacific Northwest Marine Sediment Communities
- G. Braker, Jizhong Zhou, Liyou Wu, A. Devol, J. Tiedje
- BiologyApplied and Environmental Microbiology
- 1 May 2000
Findings show a very high diversity of nirsequences within small samples and that these novel nirclusters, some very divergent from known sequences, are not known in cultivated denitrifiers.