New Bradyrhizobium japonicum Strains That Possess High Copy Numbers of the Repeated Sequence RSα

Abstract

In a survey of DNA fingerprints of indigenous Bradyrhizobium japonicum with the species-specific repeated sequences RSα and RSβ, 21 isolates from three field sites showed numerous RS-specific hybridization bands. The isolates were designated highly reiterated sequence-possessing (HRS) isolates, and their DNA hybridization profiles were easily distinguished from the normal patterns. Some HRS isolates from two field sites possessed extremely high numbers of RSα copies, ranging from 86 to 175 (average, 128), and showed shifts and duplications of nif- and hup-specific hybridization bands. The HRS isolates exhibited slower growth than normal isolates, although no difference in symbiotic properties was detected between the HRS and normal isolates. Nucleotide sequence analysis of 16S rRNA genes showed that HRS isolates were strains ofB. japonicum. There was no difference in the spectra of serological and hydrogenase groupings of normal and HRS isolates. Some HRS isolates possessed a tandem repeat RSα dimer that is similar to the structure of (IS30)2, which was shown to cause a burst of transpositional rearrangements in Escherichia coli. The results suggest that HRS isolates are derived from normal isolates in individual fields by genome rearrangements that may be mediated by insertion sequences such as RSα.

Phylogeny and distribution of extra-slow-growing Bradyrhizobium japonicum harboring high copy numbers of RSα, RSβ and IS1631

“…HRS strains of B. japonicum provide an insight to bacterial evolution with respect to generation of genetic diversity in soil and symbiotic bacteria. Since IS copy number generally increases bacterial evolution [31], HRS strains have been probably generated from non-HRS strains by transposition and recombination events [4]. The presence and correlation of HRS strains with phylogeny and serocluster (Fig.…”

“…Group B HRS strains are found in Japan, China as well as USA (see text). ¢eld-grown soybeans [4,5,7]. Macroptilium atropurpureum was well nodulated with ESG strain NK5 (Group A HRS strain), and the nodulated legumes normally grew without nitrogen supply in a experiment of horizontal gene transfer [6].…”

“…Table 2 also indicates that group A HRS strains grew very slowly (mean generation time þ S.D., 27.1 þ 8.7 h) in HM medium. The HRS group B strains and those harbor- a Serotypes determined previously [4]. b Determined previously [4].…”

“…The HRS group B strains and those harbor- a Serotypes determined previously [4]. b Determined previously [4]. c Data from Ham et al [11].…”

“…Previously, HRS strains have been found among B. japonicum cluster at three of six ¢eld sites tested in Japan [3,4,5,7]. The ESG HRS strains were dominant at the Nagakura ¢eld site, where paddy-upland rotation had been carried out for nearly 30 years [3,7].…”