Insights learned from pBTAi1, a 229-kb accessory plasmid from Bradyrhizobium sp. strain BTAi1 and prevalence of accessory plasmids in other Bradyrhizobium sp. strains

Abstract

In silico, physiological and in planta analyses were used to characterize pBTAi1, a 229-kb accessory plasmid from Bradyrhizobium sp. strain BTAi1, and assess its potential ecological function under free-living and symbiotic growth conditions. Sequence analysis revealed the presence of an uptake hydrogenase system, a repABC family plasmid replication module and open reading frames encoding type IV secretion system, TraI and TraR autoinducer proteins and several copper resistance-related proteins. Bradyrhizobium sp. BTAi1 was capable of growing in 200 mg l À1 CuCl 2 . In contrast, the closely related, plasmid-free Bradyrhizobium sp. strain ORS278 could not grow at copper concentrations exceeding 100 mg l À1 . The plasmid-localized hydrogenase genes were phylogenetically distinct from those typically found in other rhizobial species, and were most related to hup genes from Thiobacillus denitrificans. The induction of the plasmid-borne hydrogenase genes during symbiosis was significantly lower than the two chromosomal-borne hydrogenase clusters. CHEF-pulsed-field gel electrophoresis was used for a comprehensive analysis of the diversity, abundance and genetic composition of accessory plasmids in other Bradyrhizobium strains. Plasmids were detected in 11 of 46 (23.9%) geographically diverse Bradyrhizobium japonicum and Bradyrhizobium elkanii strains, isolated from the United States, China and Thailand. Plasmid size was heterogeneous, ranging from 75 to 330 kb, with only two strains (DASA01244 and DASA01265) harboring plasmids with identical (240 kb) size. None of the plasmids harbored nodulation or hydrogenase genes. Taken together, our results indicate that while plasmids having ecologically significant functions may be detected in Bradyrhizobium sp. strains, they lack genes necessary for symbioses with legumes.

Comparative genomics of Bradyrhizobium japonicum CPAC 15 and Bradyrhizobium diazoefficiens CPAC 7: elite model strains for understanding symbiotic performance with soybean

“…No plasmid replication genes were detected, indicating that CPAC 7 does not possess plasmids and that its genome is composed of a single replicon. This result is in agreement with the reported absence of plasmids in Bd strain USDA 122 [26], the parent strain of CPAC 7. In CPAC 7 there was only one ribosomal operon and the G + C content was 63.98% (Table 1, Figure 1).…”

“…In the genus Rhizobium , rearrangements are common but involve mainly plasmid replicons, whereas chromosomes are more stable [29, 30]. As genome plasticity may be related to adaptation [31], it is not surprising that Bradyrhizobium genomes also displayed rearrangements even when plasmids are relatively uncommon in this genus [26]. …”

Comparative Genomics of Aeschynomene Symbionts: Insights into the Ecological Lifestyle of Nod-Independent Photosynthetic Bradyrhizobia

“…All 10 genomes seem to be composed of a unique chromosome, except strain BTAi1 which also harbors a plasmid [19]. B. japonicum USDA110 possesses the biggest genome with a length of 9,105,828 bp, and Bradyrhizobium .…”

Biodegradation of a Biocide (Cu- N -Cyclohexyldiazenium Dioxide) Component of a Wood Preservative by a Defined Soil Bacterial Community

“…However, the analyzed pesticides and environmental conditions in these studies varied, and none of these pesticides had a chemical structure similar to that of HDO or potential metabolites. In addition, members of all of these genera were characterized as copper tolerant except those of the genus Phenylobacterium (8,11,29,32,39).…”