Bt Research 2025, Vol.16, No.2, 70-78 http://microbescipublisher.com/index.php/bt 72 2.3 Advances in bioinformatics for population genomics The development of high-throughput sequencing has led to rapid progress in Bt population genomics research. Whole genome sequencing (WGS) combined with bioinformatics analysis can systematically compare the SNP, gene content, plasmid and virulence gene distribution of Bt strains (Shikov et al., 2021). There are now many bioinformatics tools available, such as IQ-TREE, parsnp, snp-dists, which can efficiently construct core genome alignment, SNP distance matrix and phylogenetic tree, revealing evolutionary relationships and gene flow among strains (Biggel et al., 2022). Population structure analysis methods based on genomic data, such as goeBURST and PhyloViz, can also identify clonal complexes, haplotypes and new genotypes, providing technical support for the study of ecological adaptation and functional diversity of Bt (Pheepakpraw et al., 2023). 3 Population Structure of Bt Across Different Ecosystems 3.1 Agricultural ecosystems: crop rhizosphere and phyllosphere habitats In agricultural ecosystems, Bt is commonly found in microhabitats such as the rhizosphere and leaf zone of crops. Experimental evolution and whole-genome sequencing have revealed that Bt has a higher mutation frequency and genotype diversity in the rhizosphere of plants, especially in the root-related environment. This is closely related to the spatial differences and nutritional diversity brought about by plant hosts. In the rhizosphere, the adaptive evolution of Bt IS mainly influenced by the activity of the insertion sequence (IS element), which generates new genotypes and maintains population diversity (Hu et al., 2023). In addition, the genotype distribution of cry toxin in Bt strains varies greatly in soils of different crops and regions. Some strains simultaneously carry genes that are active against both Lepidoptera and Coleoptera insects, indicating that the Bt population structure in agricultural ecosystems is very complex and its functions are also very rich (Uribe et al., 2003). 3.2 Forest and natural soil ecosystems In forest and natural soil ecosystems, the genetic diversity of Bt populations is also very high. Multilocus sequence typing (MLST) studies have shown that Bt strains in forest soil can be divided into several major phylogenetic clusters (such as T clusters), which, together with related species like B. cereus, form independent clonal groups. The Bt population in forest soil is mainly composed of clonal structures. Some strains are closely related to strains adapted to low temperatures, showing obvious ecological adaptation differentiation (Sorokin et al., 2006). In the natural soil of subtropical regions, Bt strains contain more than 20 H serotypes. The host adaptability and the morphology of parasitic crystals are both rich, indicating that Bt is widely distributed in natural ecosystems and has obvious genetic differentiation (Ohba et al., 2000). 3.3 Aquatic and insect-associated environments Bt not only exists on land, but is also distributed in aquatic environments and insect-related environments. Bt strains isolated from water bodies and insects often have specific toxin genotypes and host specificity. For instance, some strains in aquatic environments can specifically kill mosquito larvae, and their parasitic crystals are often spherical or ovate (Ohba et al., 2000). In insect-related environments, the population structure of Bt is influenced by the host species and geographical distribution. There are many cases of combined distribution of cry genotypes among strains. Some strains have high insecticidal activity and are suitable for regional pest control (Uribe et al., 2003). Moreover, population evolution experiments have found that Bt adopts different adaptation strategies in different environments. The activity of biofilm formation and insertion sequences is an important mechanism for its adaptation to various environments (Hu et al., 2023). 4 Ecological Drivers of Bt Genetic Diversity 4.1 Environmental factors: soil type, climate, vegetation cover The genetic diversity of Bt is influenced by many environmental factors. The type of soil, pH value, amount of organic matter and moisture condition will all directly affect the distribution and survival of Bt. Bt strains in different soils and regions vary greatly in cry genotype and plasmid type (Vilas-Bôas and Lemos, 2004). Climatic conditions, such as temperature and precipitation, as well as vegetation coverage, can also affect the ecological niche and gene flow of Bt. Geographical isolation and environmental differences make genetic differentiation
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