Complete Genomic Structure of the Cultivated Rice Endophyte Azospirillum sp. B510

Abstract

We determined the nucleotide sequence of the entire genome of a diazotrophic endophyte, Azospirillum sp. B510. Strain B510 is an endophytic bacterium isolated from stems of rice plants (Oryza sativa cv. Nipponbare). The genome of B510 consisted of a single chromosome (3 311 395 bp) and six plasmids, designated as pAB510a (1 455 109 bp), pAB510b (723 779 bp), pAB510c (681 723 bp), pAB510d (628 837 bp), pAB510e (537 299 bp), and pAB510f (261 596 bp). The chromosome bears 2893 potential protein-encoding genes, two sets of rRNA gene clusters (rrns), and 45 tRNA genes representing 37 tRNA species. The genomes of the six plasmids contained a total of 3416 protein-encoding genes, seven sets of rrns, and 34 tRNAs representing 19 tRNA species. Eight genes for plasmid-specific tRNA species are located on either pAB510a or pAB510d. Two out of eight genomic islands are inserted in the plasmids, pAB510b and pAB510e, and one of the islands is inserted into trnfM-CAU in the rrn located on pAB510e. Genes other than the nif gene cluster that are involved in N2 fixation and are homologues of Bradyrhizobium japonicum USDA110 include fixABCX, fixNOQP, fixHIS, fixG, and fixLJK. Three putative plant hormone-related genes encoding tryptophan 2-monooxytenase (iaaM) and indole-3-acetaldehyde hydrolase (iaaH), which are involved in IAA biosynthesis, and ACC deaminase (acdS), which reduces ethylene levels, were identified. Multiple gene-clusters for tripartite ATP-independent periplasmic-transport systems and a diverse set of malic enzymes were identified, suggesting that B510 utilizes C4-dicarboxylate during its symbiotic relationship with the host plant.

Distinct Domains of CheA Confer Unique Functions in Chemotaxis and Cell Length in Azospirillum brasilense Sp7

“…None of the other Azospirillum species strains sequenced to date shows evidence of a similar domain insertion (34)(35)(36)(37)(38)(39). In fact, the draft genome of an Sp7 strain generated by a team of South Korean scientists also lacks the TMX fusion to CheA1 (NCBI BioProject PRJNA293508).…”

“…In fact, the draft genome of an Sp7 strain generated by a team of South Korean scientists also lacks the TMX fusion to CheA1 (NCBI BioProject PRJNA293508). A. brasilense genomes are organized as 7 replicons: one chromosome and 6 large plasmids named p1 through p6 (34)(35)(36)(37)(38)(39). The DNA regions coding for CheA1 and for TMX are both located on the largest plasmid, p1, in all A. brasilense strains with available genome sequences, but they are not adjacent and are separated by several kilobases, precluding a simple frameshifting or slippage mutation between adjacent genes.…”

Identification and isolation of active N2O reducers in rice paddy soil

“…. However, it is also possible that these strains lack a nitrite reduction pathway as nirK of several Azospirillum strains is located on plasmids (Pothier et al, 2008;Kaneko et al, 2010).…”

Azospirillum sp. Strain B510 Enhances Rice Growth and Yield

“…Primers used in the primary reaction were 5'-TTGAGGGTCCGGCATCAG-3' and 5'-TCAGGAAGTCCGTATGGCGTT-3', and those in the sec-ondary reaction were 5'-CGTCCCTCGACACCAGCAC-3' and 5'-GTCGCCTTGTGGGCTTGC-3', designed from the sequence of the 16S-23S internal transcribed spacer (ITS) region of strain B510 (Accession No. AP010947) (10). PCRs were run in 25-µL volumes containing 10 µL (primary reaction) or 2 µL (secondary reaction) of template, 2 pmol primers, 1.5 mM magnesium chloride, 200 µM dNTPs, and 0.1 U of Taq DNA polymerase (Takara Bio, Otsu, Japan).…”