INVITED REVIEW: Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances

  title={INVITED REVIEW: Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances},
  author={Jianping Xu},
  journal={Molecular Ecology},
  • Jianping Xu
  • Published 1 June 2006
  • Biology
  • Molecular Ecology
Microbial ecology examines the diversity and activity of micro‐organisms in Earth's biosphere. In the last 20 years, the application of genomics tools have revolutionized microbial ecological studies and drastically expanded our view on the previously underappreciated microbial world. This review first introduces the basic concepts in microbial ecology and the main genomics methods that have been used to examine natural microbial populations and communities. In the ensuing three specific… 

Metagenomics: A Relief Road to Novel Microbial Genes and Genomes

This chapter will deal with the techniques used in metagenomics and achievements made so far along with future applications and challenges.

Overview of Metagenomics for Marine Biodiversity Research

Interdisciplinary approaches will be required to fully understand microbial ecology by: (1) analysis of genomes, transcriptomes, proteomes and metabolomes and (2) analysis at various levels of individuals, populations, communities and ecosystems.

Microbial systematics in the post-genomics era

Two kinds of molecular markers consisting of conserved indels in protein sequences and whole proteins that are specific for different groups that are proving particularly valuable in defining different prokaryotic groups in clear molecular terms and in understanding their interrelationships are described.


The purpose of this paper was to bring in front the discipline of metagenomics which will be used in many scientific areas in the future, and to describe MG-RAST software as bioinformatics method that is suitable for usage in ecological studies.

The integration of sequencing and bioinformatics in metagenomics

The emergence of new technologies based on sequencing environmental DNA and on bioinformatics are reviewed to assess its potential for application in environmental studies, particularly for developing new biomolecules that can be applied to degrading recalcitrant pollutants in terrestrial and aquatic systems.

The Positive Role of the Ecological Community in the Genomic Revolution

This commentary reviews three initiatives presented in the “new frontiers” session of the second SCOPE meeting on Microbial Environmental Genomics (MicroEnGen-II, Shanghai, June 12–15, 2006) and underscores the increasingly important role ecologists have to play in the genomic (metagenomic) revolution.

Bioinformatics tools to assess metagenomic data for applied microbiology

An overview of the evolution of knowledge of microbial ecology from traditional culture-dependent methods to culture-independent methods and the last frontier in knowledge, metagenomics is presented.

Marine Microbial Metagenomics: From Individual to the Environment

This work reviews studies investigating microbial genomics at the individual and community levels to summarize the current understanding of microbial ecology in the environment.

Understanding microbially active biogeochemical environments.




Novel techniques for analysing microbial diversity in natural and perturbed environments.

Community structure and metabolism through reconstruction of microbial genomes from the environment

Reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II and analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment.

Microbial genomes

There will be an increasing need for us to explore the detailed implications of genomic findings and Bioinformatics, twinned with the new experimental approaches forming ‘functional genomics’, provides some of the needed tools.

Community genomics in microbial ecology and evolution

Genomics can reveal how individual species and strains contribute to the net activity of the community and enable subsequent gene expression and proteomic studies to determine how resources are invested and functions are distributed among community members.

Microbial community genomics in the ocean

  • E. Delong
  • Environmental Science
    Nature Reviews Microbiology
  • 2005
Ocean-going genomic studies are now providing a more comprehensive description of the organisms and processes that shape microbial community structure, function and dynamics in the sea, and are poised to reveal the fundamental principles that drive microbial ecological and evolutionary processes.

Genomic insights that advance the species definition for prokaryotes.

The average nucleotide identity of the shared genes between two strains was found to be a robust means to compare genetic relatedness among strains, and that ANI values of approximately 94% corresponded to the traditional 70% DNA-DNA reassociation standard of the current species definition.

Prospecting for Novel Biocatalysts in a Soil Metagenome

The metagenome of a mixed microbial population was exploited for isolation of more than 15 different genes encoding novel biocatalysts by using a combined cultivation and direct cloning strategy and more than 162 kb of DNA sequence is described that provides a strong platform for further characterization of this microbial consortium.

Novel kingdom-level eukaryotic diversity in anoxic environments

  • S. DawsonN. Pace
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 2002
A cultivation-independent, molecular phylogenetic survey of three anoxic sediments found many previously unrecognized eukaryotes, including representatives of seven lineages that are not specifically related to any known organisms at the kingdom-level and branch below the Eukaryotic “crown” radiation of animals, plants, fungi, stramenopiles, etc.

Genetic diversity in Sargasso Sea bacterioplankton

The phylogenetically analysed clone libraries of eubacterial 16S ribosomal RNA genes amplified from natural populations of Sargasso Sea picoplankton indicate the presence of a novel microbial group, the SAR 11 cluster, which appears to be a significant component of this oligotrophic bacterioplankton community.

Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications.

CGA hybridization has potential as a specific, sensitive, and quantitative tool for detection and identification of microorganisms in environmental samples, and reveals differences in microbial community composition in soil, river, and marine sediments.