Developing Genomic Analysis Strategies for Bacterial Species Complexes

What is taxonomy?

Humans require a universal classification and naming system to comprehend the complexities of the world and communicate with each other. For instance, when engineers discuss machine parts, they must utilize well-defined part categories and names to understand one another. However, in addition to the standardized formal names, machine parts may have alternative names or common names. It is important for these names to be consistent and widely accepted for effective communication. If a part has multiple names and each engineer knows only a few of them, communication among the group will be challenging. Similarly, if a part’s name is frequently changed or different parts have identical or similar names, it will create communication difficulties.

Likewise, taxonomy is a system for naming and organizing biological entities, such as different plants and animals, into groups that share similar qualities. This system allows biologists to communicate effectively and facilitate the accumulation of knowledge.

What is the purpose of taxonomy?

Taxonomy affects our lives in several ways:

1. Medical Diagnosis:

When infectious diseases occur, clear communication about the causative pathogen is essential for doctors, medical personnel, and patients to determine the appropriate treatment according to existing knowledge.

2. Epidemic Prevention and Quarantine:

The prevalence of international trade has made it easier for various pathogens or invasive species to spread between different countries, causing substantial economic losses and environmental impacts. The “Identification” part of taxonomy is a crucial tool for quarantine authorities to confirm the identity of incoming organisms and provide an essential foundation for effective control.

3. Ecological Conservation:

Accurate species delineation enables us to explore the composition and function of ecosystems, leading to the development of corresponding conservation plans and management measures that promote balance and sustainability. Additionally, delineating rare species serves as a fundamental basis for conservation policies that effectively safeguard biodiversity.

What is a species complex? What makes it unique in taxonomy?

In biology, a species complex is a group of closely related organisms that are similar in appearance and other features such that the boundaries among them are often unclear. Classifying these organisms as a single species and giving them the same name would result in the name being used for organisms that are not so similar. On the other hand, dividing the group into several different species for accurate categorization may be difficult. Such situations create communication difficulties in both basic science and practical applications. Notably, with the advancement of science, many bacteria closely related to our daily lives have been found to be species complexes.

New insights into the taxonomy of bacterial species complexes

The research team led by Dr. Chih-Horng Kuo at the Institute of Plant and Microbial Biology, Academia Sinica has devised genomic analysis strategies for investigating genome diversity applicable to bacterial species complexes by using Agrobacterium tumefaciens as a study system. The research process and findings are as follows:

1. First, select representative strains within a species complex for whole-genome sequencing, and compare the DNA sequences and gene content among all strains to identify similarities and differences. This analysis can establish a quantitative species definition method that clearly distinguishes several different species within a complex, which allows assignment of new names to each newly defined species. This method can also be applied to identify newly isolated strains in the future. In addition, genome analysis can also be used to explore the evolutionary relationships among different species and strains within a species complex.

2. Once species delimitation and evolutionary relationships are established, the genetic diversity and evolutionary history of specific genes can be investigated. In this study, the type VI secretion system (T6SS) genes were selected for analysis as they play a crucial role in pathogenesis, symbiosis, and inter-bacterial competition. The results revealed that the T6SS genes exhibit a high level of diversity and complex evolutionary histories, even among closely related species within the same species complex. Some species have lost these genes during evolution, leading to genetic differences among closely related species. Furthermore, one species even regained these genes from another closely related species after losing them. The ability of bacteria to continuously lose or acquire genes during evolution, rather than relying solely on gradual accumulation of mutations, is a key factor for their rapid evolution.

3. A. tumefaciens is important as a plant pathogen and a biotechnology tool for genetic transformation. In both cases, the function depends on the tumor-inducing plasmids (pTi) of this bacterium. Therefore, the research team investigated these plasmids to learn more about them. The results revealed that the evolution of these plasmids is different from that of the chromosome, which may be a key factor in the rapid evolution and adaptation of A. tumefaciens to different plant hosts. It was also discovered that these plasmids can be exchanged between different bacteria, a mechanism similar to the rapid evolution of drug resistance in other pathogens.

4. The findings of this new study indicated that genomic analysis can clearly delineate the species boundaries within a species complex based on DNA sequences or gene content, which allows for the investigation of genetic differentiation at the among- and within-species levels.

References: Chou et al. (2022) Modular evolution of secretion systems and virulence plasmids in a bacterial species complex. BMC Biology 20:16

From species delineation to a new chapter in scientific research

A. tumefaciens is an important plant pathogen. By classifying and analyzing its genome, we can gain valuable insights into its basic biology and promote future applied research. The findings can facilitate future functional studies of A. tumefaciens, and the newly developed strategies for multi-level genomic analysis are applicable to other bacterial species complexes. From a broader perspective, this can also advance the fields of genomics and evolutionary biology.


What is Agrobacterium tumefaciens?

A. tumefaciens is a bacterium commonly found in soil. It has the ability to infect plant cells and transfer a specific sequence of its own DNA to the plant cells. This DNA transfer can cause the plant cells to form tumors, resulting in a condition known as crown gall disease. Although the growth of tumors on plants is typically not fatal, it can lead to reduced yields in fruit trees and render cuttings used for propagation unsellable.

What is the application of Agrobacterium tumefaciens?

A. tumefaciens has a wide range of applications, with the most well-known being the creation of genetically modified (GM) crops. Scientists can modify the tumor-inducing plasmid of A. tumefaciens by replacing the DNA segment it usually inserts into the plant with a different sequence, allowing for the creation of plants that express specific desired traits. For example, by transferring herbicide-resistant genes to specific crops using A. tumefaciens and breeding new varieties, weeds can be eliminated in the field using the herbicide without harming the crops.

Additionally, A. tumefaciens is a critical tool for genetic manipulation in plant sciences, making it an important resource for basic research aiming at understanding the function of specific genes. The knowledge obtained through such research can also be applied to traditional breeding methods to develop new plant varieties that improve human life.