Draft Genome Sequence of the Nitrogen-Fixing Symbiotic Bacterium Bradyrhizobium elkanii 587

Abstract

The draft sequence of the genome of Bradyrhizobium elkanii 587 is presented. This was obtained using Illumina Next-Gen DNA sequencing combined with Sanger sequencing. Genes for the pathways involved in biological nitrogen fixation (the nif gene cluster), nod genes including nodABC, and genes for the type III protein secretion system (T3SS) are present. Bradyrhizobium elkanii 587 is a nitrogen-fixing bacterium that nodulates soybean and is used in commercial inoculants in Brazil (7).The draft genome sequence of B. elkanii 587 was obtained using a combination of Illumina and Sanger reads. A total of 6,020,858 endpaired reads were de novo assembled using Velvet (11) with an average read depth of 28-fold; 42,785 Sanger reads were added to the assembly, resulting in 260 scaffolds (N 50 , 54,941 bp). Scaffold ordering was carried out using Bradyrhizobium japonicum USDA110 as a reference. B. elkanii 587 contains one circular chromosome of 8.8 Mbp with a GϩC content of 62.9%, and no plasmid was detected. Annotation of 9,250 potential open reading frames (ORFs) and 71 tRNA genes was performed using the RAST program (1). Genes of interest were curated and analyzed manually. A single rRNA operon was found, as in B. japonicum USDA110 (4).Genes for the same metabolic pathways found in B. japonicum were found in the genome of B. elkanii 587. Genes encoding the Entner-Doudoroff and Embden-Meyerhof-Parnas pathways for carbohydrate degradation are present.The nif genes nifDKENX-(orf1 to orf7)- fixBCX are present in one cluster. The genes related to nodulation are organized in two regions. The first contains 19 genes, nodUIJ, nopM, nodZ, fixR, nifA, nopM, fixAKLNOGHI, noeE, and nodQP, and includes the nif transcriptional activator (the nifA gene). The second cluster contains five genes, nodD1 and nodABCS. The genes nodT, nopB, nodU, nolY, nolL, and nolV were identified outside the clusters.

Commonalities and differences of T3SSs in rhizobia and plant pathogenic bacteria

“…Similarly, the draft sequence of the genome of B. elkanii 587 revealed the presence of a tts gene cluster similar to that found in B. elkanii USDA 61 (de Souza et al, 2012). Both B. elkanii T3SSs possess nopX , which is absent in the close relative B. japonicum , but it is present in S. fredii strains (Figure 3).…”

Isolation of Novel Afipia septicemium and Identification of Previously Unknown Bacteria Bradyrhizobium sp. OHSU_III from Blood of Patients with Poorly Defined Illnesses

“…Interestingly, the sequence comparison revealed that none of the nif and nod genes or Symbiosis Islands found in genomes of B. elkanii, B. japonicum and other nitrogen-fixation Bradyrhizobium sp. isolated from soil or plants [18], [28] are present in the genome of OHSU_III. We plan to continue the cultures of the microbes that are alive but in a less-active state in OHSU_III culture.…”

Comparative symbiotic plasmid analysis indicates that symbiosis gene ancestor type affects plasmid genetic evolution

“…Genes associated with the symbiotic lifestyle in most of the Bradyrhizobium species are located in their chromosome, with the exception of Bradyrhizobium sp. DOA9 strain, which harbours a 0Á74 Mb symbiotic plasmid containing genes involved in nodulation, nitrogen fixation and type III/IV protein secretion systems (Kaneko et al 2002;de Souza et al 2012;Okazaki et al 2015). Even in the Mesorhizobium species, symbiotic plasmids only could be found in Mesorhizobium huakuii and Mesorhizobium amorphae strains (Kaneko et al 2000;Reeve et al 2013;Wang et al 2014;Haskett et al 2016).…”