Microbial systematics in the post-genomics era

Abstract

Microbial systematics and phylogeny should form the foundation and guiding light for a comprehensive understanding of different aspects of microbiology. However, there are many critical issues in microbial systematics that are currently not resolved. Some of these include: how to define and delimit a prokaryotic species; development of rationale criteria for the assignment of higher taxonomic ranks; understanding what unique properties distinguish species from different groups; and understanding the branching order and interrelationship among higher prokaryotic clades. The sequencing of genomes from large numbers of cultured as well as uncultured microbes covering prokaryotic diversity provides unique means to achieve these important objectives. Prokaryotic genomes are found to be very diverse and dynamic and horizontal gene transfers (HGTs) are indicated to have played important role in species/genome evolution. Although HGT adds a layer of complexity in terms of understanding the genomes and species evolution, it is contended that vast majority of genes and genetic characteristics that are distinctive characteristics of higher prokaryotic taxa are vertically inherited and based on them a solid foundation for microbial systematics can be developed. We describe 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. The genetic and biochemical studies on these taxa-specific molecular markers also open the way to discover novel biochemical and physiological characteristics that are unique properties of these groups.

Molecular signatures for the class Coriobacteriia and its different clades; proposal for division of the class Coriobacteriia into the emended order Coriobacteriales , containing the emended family Coriobacteriaceae and Atopobiaceae fam. nov., and Eggerthe

“…Thus, these CSIs represent molecular synapomorphies depicting the shared evolutionary histories of these taxa and they provide novel and reliable means to distinguish these groups of bacteria in molecular terms. Our earlier work on other CSIs has shown that they are highly specific characteristics of different bacterial groups and they retain their group-specificity as sequence information from additional taxa is obtained (Gao & Gupta, 2005;2012a, b;Gupta, 2009). Thus, based upon the presence or absence of these CSIs, new members belonging to these taxa can be identified and inducted into different clades of the class Coriobacteriia.…”

“…Many of these genomes were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea project (Wu et al, 2009;Copeland et al, 2009;Mavrommatis et al, 2009;Pukall et al, 2009;Saunders et al, 2009;Göker et al, 2010). These genome sequences allow us to reconstruct a robust phylogenetic tree for the members of the class Coriobacteriia for which sequences are available based upon concatenated sequences of multiple conserved proteins (Rokas et al, 2003;Wu et al, 2009;Gao & Gupta, 2012b also supported by phylogenetic analyses (Gupta, 1998(Gupta, , 2001Gao & Gupta, 2012a …”

Bacterial Genome Instability

“…Several studies have concluded that, depending on the bacterial strain, up to 20% of genes in a prokaryotic genome were recently introduced by HGT (459,508,509). According to Dutta and Pan, these numbers are underestimates, whereas they are overestimates for Kurland and collaborators and for Gao and Gupta (464,483,510,511). In addition, a study of 181 sequenced prokaryotic genomes indicated that at least 81% of the genes in each of these genomes had been involved in HGT at one point in their history (512).…”

“…Therefore, a number of scientists think that origins and relationships between prokaryote species cannot be represented as a tree and have proposed various alternative ways to describe the evolution of bacteria and life, usually as a forest, a network, or a ring (473,516,(574)(575)(576)(577)(578)(579)(580)(581). Conversely, numerous scientists think that the universal tree might still be an appropriate concept and have succeeded in constructing a tree of life despite or even based on HGT (468,483,511,518,561,(582)(583)(584)(585)(586)(587)(588)(589)(590)(591). Remarkably, as well as being used to construct phylogenetic trees, 16S rRNAs were used by microbial ecologists to predict the ecological functions of a microbe.…”

“…Some new microorganism-specific classification systems have even been proposed (475,598). However, other scientists argue that the complexity added by HGT does not impede the classification of bacteria within species, as the vast majority of a bacterial genome is still vertically inherited (457,483).…”