Multilocus sequence analysis (MLSA) represents the novel standard in microbial molecular systematics. In this context, MLSA is implemented in a relatively straightforward way, consisting essentially in the concatenation of several sequence partitions for the same set of organisms, resulting in a "supermatrix" which is used to infer a phylogeny by means of distance-matrix or optimality criterion-based methods. This approach is expected to have an increased resolving power due to the large number of characters analyzed, and a lower sensitivity to the impact of conflicting signals (i.e. phylogenetic incongruence) that result from eventual horizontal gene transfer events. The strategies used to deal with multiple partitions can be grouped in three broad categories: the total evidence, separate analysis and combination approaches. The concatenation approach that dominates MLSAs in the microbial molecular systematics literature is known to systematists working with plants and animals as the "total molecular evidence" approach, and has been used to solve difficult phylogenetic questions such as the relationships among the major groups of cetaceans, that of microsporidia and fungi, or the phylogeny of major plant lineages. The total molecular evidence approach has been criticized because by directly concatenating all available sequence alignments, the evidence of conflicting phylogenetic signals in the different data partitions is lost along with the possibility to uncover the evolutionary processes that gave rise to such contradictory signals. The nature of these conflicts is varied, but in the microbial world the strongest conflicting signals often derive from the existence of horizontal gene transfer events in the dataset. If the individuals containing xenologous loci are not identified and removed from the supermatrix prior to phylogeny inference, the resulting hypothesis may be strongly distorted, since standard treeing methods assume a single underlying evolutionary history. Based on these arguments, the conditional data combination strategy is to be generally preferred in bacterial MLSA read more ...

from Molecular Phylogeny of Microorganisms by Aharon Oren and R. Thane Papke (2010)

References

• Molecular Phylogeny of Microorganisms
• Lab-on-a-Chip Technology
• Real-Time PCR: Current Technology and Applications
• Environmental Molecular Microbiology
• Metagenomics

Labels: horizontal gene transfer, Microbial molecular systematics, MLSA, Multilocus sequence analysis, Phylogenetic incongruence, Phylogeny

A new update on research in Microbial Ecology

Microbial Diversity and Phylogeny
Genomics and Metagenomics
Metaproteomics
Nucleic-Acid-based Characterization
Microarrays in Microbial Ecology
The Soil Environment
Plant Microbial Communities
Marine Microbial Environments
Ocean microbial communities
Human Microbial Environment
Wastewater Treatment
Bacterial Biofilms

Read more at: Microbial Ecology

Labels: Bacterial Biofilms, ecology, genomics, metagenomics, Metaproteomics, microarrays, microbial communities, Microbial Diversity, Microbial Environments, Phylogeny, Soil Environment, Wastewater

The small subunit ribosomal RNA gene (SSU rRNA) has been the cornerstone of microbial ecology studies over the last 15 years, and has provided much of what we know about Bacterial and Archaeal diversity and community structure, and has greatly aided microbial taxonomy. Genomics is aiding our understanding of the relationships among closely related organisms, and ultimately of natural populations.

In a recent study the available 16S rRNA genes from species type strains were examined. The most distant sequences in the median genus and family were about 4.4% and 14% different, respectively. The largest dissimilarity between a sequence and its closest relative in the same taxa (similar to single-linkage clustering distance) was 3.5% and 10% for the median genus and family. The ratio of the two values averaged less than 1.5 for all ranks, indicating that most taxa are not elongated, but are fairly spherical. When the near-full-length 16S rRNA gene sequences in the public databases were clustered into groups at proxy distances for species, genus, family and order, the number of clusters with time increased exponentially for all ranks documenting the enormous diversity of the microbial world.

from James R. Cole, Kostas Konstantinidis, Ryan J. Farris and James M. Tiedje in Environmental Molecular Microbiology

Further reading:

• Environmental Molecular Microbiology
• Metagenomics: Theory, Methods and Applications
• Environmental Microbiology

Labels: Archaeal diversity, Microbial Diversity, Microbial taxonomy, Phylogeny