Burkholderia cepacia is regarded as a genetically distinct but phenotypically similar bacteria group referring to Burkholderia cepacia complex （Bcc）, which is found not only in clinic but also in rice growing enviro...Burkholderia cepacia is regarded as a genetically distinct but phenotypically similar bacteria group referring to Burkholderia cepacia complex （Bcc）, which is found not only in clinic but also in rice growing environment. It is very important in microbial safety of rice for us to understand the genomovar status of Bcc. Genomovar analysis was performed among 87 Bcc isolates by means of Hae Ⅲ-recA RFLP assays and species-specific PCR tests. Three genomovars were found from the rice rhizosphere including Ⅰ, ⅢB and V, and genomovar V was predominant. Genomovars Ⅰ, ⅢA and ⅢB existed in the clinical samples, and genomovar ⅢA was the most popular. It showed that genomovar composition was different between the Bcc strains from the rice rhizosphere and clinical environment. Simultaneously, the results revealed the genetic diversity of Bcc strains from the rice rhizosphere, and genomovar Ⅲ referred as virulent species in clinic also existed in the rice rhizosphere.展开更多
Whether prokaryotes,and other microorganisms,form distinct clusters that can be recognized as species remains an issue of paramount theoretical as well as practical consequence in identifying,regulating,and communicat...Whether prokaryotes,and other microorganisms,form distinct clusters that can be recognized as species remains an issue of paramount theoretical as well as practical consequence in identifying,regulating,and communicating about these organisms.In the past decade,comparisons of thousands of genomes of isolates and hundreds of metagenomes have shown that prokaryotic diversity may be predominantly organized in such sequence-discrete clusters,albeit organisms of intermediate relatedness between the identified clusters are also frequently found.Accumulating evidence suggests,however,that the latter“intermediate”organisms show enough ecological and/or functional distinctiveness to be considered different species.Notably,the area of discontinuity between clusters often—but not always—appears to be around 85%–95%genome-average nucleotide identity,consistently among different taxa.More recent studies have revealed remarkably similar diversity patterns for viruses and microbial eukaryotes as well.This high consistency across taxa implies a specific mechanistic process that underlies the maintenance of the clusters.The underlying mechanism may be a substantial reduction in the efficiency of homologous recombination,which mediates(successful)horizontal gene transfer,around 95%nucleotide identity.Deviations from the 95%threshold(e.g.,species showing lower intraspecies diversity)may be caused by ecological differentiation that imposes barriers to otherwise frequent gene transfer.While this hypothesis that clusters are driven by ecological differentiation coupled to recombination frequency(i.e.,higher recombination within vs.between groups)is appealing,the supporting evidence remains anecdotal.The data needed to rigorously test the hypothesis toward advancing the species concept are also outlined.展开更多
文摘Burkholderia cepacia is regarded as a genetically distinct but phenotypically similar bacteria group referring to Burkholderia cepacia complex （Bcc）, which is found not only in clinic but also in rice growing environment. It is very important in microbial safety of rice for us to understand the genomovar status of Bcc. Genomovar analysis was performed among 87 Bcc isolates by means of Hae Ⅲ-recA RFLP assays and species-specific PCR tests. Three genomovars were found from the rice rhizosphere including Ⅰ, ⅢB and V, and genomovar V was predominant. Genomovars Ⅰ, ⅢA and ⅢB existed in the clinical samples, and genomovar ⅢA was the most popular. It showed that genomovar composition was different between the Bcc strains from the rice rhizosphere and clinical environment. Simultaneously, the results revealed the genetic diversity of Bcc strains from the rice rhizosphere, and genomovar Ⅲ referred as virulent species in clinic also existed in the rice rhizosphere.
基金supported by the Us National Science Foundation (Awards Nos.1759831 and 2129823).
文摘Whether prokaryotes,and other microorganisms,form distinct clusters that can be recognized as species remains an issue of paramount theoretical as well as practical consequence in identifying,regulating,and communicating about these organisms.In the past decade,comparisons of thousands of genomes of isolates and hundreds of metagenomes have shown that prokaryotic diversity may be predominantly organized in such sequence-discrete clusters,albeit organisms of intermediate relatedness between the identified clusters are also frequently found.Accumulating evidence suggests,however,that the latter“intermediate”organisms show enough ecological and/or functional distinctiveness to be considered different species.Notably,the area of discontinuity between clusters often—but not always—appears to be around 85%–95%genome-average nucleotide identity,consistently among different taxa.More recent studies have revealed remarkably similar diversity patterns for viruses and microbial eukaryotes as well.This high consistency across taxa implies a specific mechanistic process that underlies the maintenance of the clusters.The underlying mechanism may be a substantial reduction in the efficiency of homologous recombination,which mediates(successful)horizontal gene transfer,around 95%nucleotide identity.Deviations from the 95%threshold(e.g.,species showing lower intraspecies diversity)may be caused by ecological differentiation that imposes barriers to otherwise frequent gene transfer.While this hypothesis that clusters are driven by ecological differentiation coupled to recombination frequency(i.e.,higher recombination within vs.between groups)is appealing,the supporting evidence remains anecdotal.The data needed to rigorously test the hypothesis toward advancing the species concept are also outlined.
