MLST/A Multilocus Sequence Typing/Analysis
strengths and weaknesses of molecular approaches
explain phylogenomic concept
explain adaptive divergence
This review of bacterial classification systems includes a look at how species have been taxonomically defined in the past, and how, with the input of an ever-increasing bank of genomic data, scientists can plan to move forward in a cohesive way. As research and technology delve deeper into bacterial genomics, new insight reveals that phenotypically similar organisms may be much more diverse than they appear . Additional information, with little understanding or agreement of how to best use it, has scientists proposing new ideas at a rapid rate. Just as no one owns the taxonomic tree of life, decision making on the subject is often based on experience, reading, research and differing levels of comprehension but this suggests much more subjectivity than actually exists, in spite of debates about which concept is best. Bergey’s Manual of Systematic Bacteriology has been instrumental in helping scientists compile taxonomic data and establish hypotheses, and is a good resource for understanding the Bacterial domain, as is the book The Prokaryotes, which evaluates much of the known growth information on both bacteria and archaea .
Without a succinct, universally-accepted definition of the term species, information in scientific articles may not be properly understood by each reader in the same way. For clarity and consistency of knowledge, a clear identification of what constitutes a species is imperative, as is the recognition that this definition will continue to evolve as additional discoveries, research, and data become available. One of the best ways available to evaluate a potential new species is to publish as much information as possible in a respected research journal. Prior to inclusion in a scientific journal, other scientists and researchers review the data and help to ensure its reliability. Once published, readers can learn about the organism or even compare their own research to understand the differences and similarities .
Review of the term species and how it relates to prokaryotic classifications
As scientific discoveries progress, the foundations of ideas once considered stable can begin to crumble. In these times, new information often adds to or replaces the old. However, when this new information challenges accepted norms and complicates a standard decision making processes, the issue can be time consuming to overcome. The growth of technology, specifically DNA and RNA sequencing, has bombarded the scientific community with new data . Now, scientists must determine if this dictates an adjustment to the controversial identification of prokaryotic species – possibly wrecking some of the already established taxonomy, specifically that of prokaryotic life .
In a 2009 issue of Microbe, James T. Staley, PhD. suggests that species, as they relate to the planet’s many prokaryotes, have not been clearly defined. With additional explanations on the many ideas, techniques, and procedures used to identify classes of bacteria, Staley shows that development of taxonomy is more a process of adding in information as it becomes available, than a simple filing and categorization system . The 2012 edition of Brock Biology of Microorganisms references more than 7,000 species of bacteria and archaea and 80 different phyla established from bacterial sampling, research, and categorization, and explains how scientists have determined that prokaryotes existed first – simply because “major eukaryotic organelles clearly originated from within the domain Bacteria.” It defines “a prokaryotic species … as a group of strains sharing a high degree of similarity in several independent traits,” listing the DNA-DNA hybridization and 16SrRNA gene sequencing as the most important considerations .
Margaret A. Riley, PhD. and Michelle Lizotte-Waniewski, PhD. considered the ability of bacteria to transfer genes between species as a possible problem in the determination of which organisms belong to which species groups, and if a given? species can exist separate from all other species . With this in mind, it seems the more information available, the more complicated the decision becomes. Michael Vos considered genomic data gathered from 16s rDNA and DNA-DNA hybridization. These techniques help classify organisms based on the quantitative amount of similarities in DNA patterns. He adds to the discussion that this process can result in inaccuracies when scientists compare species without an understanding that they may have diverged over time and that these species may continue to change after the research concludes . Many researchers use the technique in tandem with small subunit rRNA, as an addition to the dataset, rather than something from which they can draw a definitive evolutionary or phylogenetic conclusion .
Alteration of the scientific classification systems is not a new phenomenon. Scientists once recognized five categories of organisms, which included: animals, bacteria, fungi, plants, and protists, but with the addition of sequenced DNA, determined that all living organisms can be placed into one of three core domains – Archaea, Bacteria, and Eukarya . Even within these three categories, organism identification has evolved. “Over the past three centuries since their discovery, bacteria have been classified in numerous ways based on morphological, serological, biochemical or genetic properties, with the species being defined differently according to the method used for the classification,” states Tang, (et. al.) in an issue of BMG Genomics .
In the past, microbes have been classified based on phenotype, behavior, and how they affect eukaryotic organisms. For instance, as Tang (et. al.) explained, Salmonella gallinarum and Salmonella pullorum, seem similar from a genetic standpoint. However, they each cause very different avian diseases. S. gallinarum causes the bird version of typhoid fever, while S. pullorum causes intense dysentery. Classification systems have kept them closely linked, even to the level of subspecies. But this extreme difference in pathology may suggest that they are essentially different species. Tang’s (et. al.) research showed genetic divergence and very specific mutation differences in the two microbes .
As the world begins to better understand the genomic roots of its eukaryotic population and considers similar evolutionary data associated with microbes, it becomes obvious that there are some very important differences. For instance, the potential for horizontal gene transfer brings up additional questions on whether a species definition has validity. According to Riley and Lizotte-Waniewski, because genetic information can so easily flow from one cell to another through conjugation, scientists may not be able to assume that all – or even a majority of – a microbe’s DNA is actually its own.  How then can that information be used as a system of classification? Riley and Lizotte-Waniewski answer their own question with an explanation of the Core Genome Hypothesis, which proposes that not all information in a microbe’s genomic makeup is able to pass in or out, but that these core genes are stable “species-specific phenotypic clusters” that maintain an organism’s required phenotypic traits and therefore its identity .
As the price of technology decreases, even more information will become readily available . Paired with continued research and joint efforts to establish development of an agreed upon prokaryotic species definition, perhaps science can converge upon a new protokaryotic identity – once which includes phylogeny and genomics to benefit continued understanding. To expand upon species defined by Madigan (et. al.) as “an interbreeding population of organisms that is reproductively isolated form other interbreeding populations,” will lend more credibility to the future of established prokaryotic systematics and further benefit research efforts .
- Madigan, M. T., Martinko, J. M., Stahl, D. A., & Clark, D. P. (2012). Chapter 16: Microbial Evolution and Systematics. In Brock biology of microorganisms (13. ed., global ed.). San Francisco, CA: Pearson Education, Inc. publishing as Benjamin Cummings.
- Riley, M., & Lizotte-Waniewski, M. (2009). Population genomics and the bacterial species concept. Methods in Molecular Biology (Clifton, N.J.), 532367-377. doi:10.1007/978-1-60327-853-9_21
- Staley, J. (2009). The phylogenomic species concept for bacteria and archaea. Microbe Magazine, 4(8). Retrieved from www.MicrobeMagazine.org.
- Tang L, Li Y, Deng X, Johnston RN, Liu GR, et al. (2013) Defining natural species of bacteria: clear-cut genomic boundaries revealed by a turning point in nucleotide sequence divergence. BMC Genomics 14: 489.
- Vos, M. (2011). A species concept for bacteria based on adaptive divergence. Trends in Microbiology, 19(1), 1-7. doi:10.1016/j.tim.2010.10.003