Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72

Abstract

Azoarcus sp. strain BH72, a mutualistic endophyte of rice and other grasses, is of agrobiotechnological interest because it supplies biologically fixed nitrogen to its host and colonizes plants in remarkably high numbers without eliciting disease symptoms. The complete genome sequence is 4,376,040-bp long and contains 3,992 predicted protein-coding sequences. Genome comparison with the Azoarcus-related soil bacterium strain EbN1 revealed a surprisingly low degree of synteny. Coding sequences involved in the synthesis of surface components potentially important for plant-microbe interactions were more closely related to those of plant-associated bacteria. Strain BH72 appears to be 'disarmed' compared to plant pathogens, having only a few enzymes that degrade plant cell walls; it lacks type III and IV secretion systems, related toxins and an N-acyl homoserine lactones-based communication system. The genome contains remarkably few mobile elements, indicating a low rate of recent gene transfer that is presumably due to adaptation to a stable, low-stress microenvironment.Endophytic bacteria reside within the living tissue of plants without substantively harming them. They are of high interest for agrobiotechnological applications, such as the improvement of plant growth and health, phytoremediation 1 or even as biofertilizer 2 . Supply of nitrogen derived from fixation of atmospheric N 2 by grass endophytes, such as Gluconacetobacter diazotrophicus and Azoarcus sp. strain BH72, which has been shown to occur in sugarcane 3 and Kallar grass 2 , is a process of potential agronomical and ecological importance.Although the lifestyle of these endophytes is relatively well documented, the molecular mechanisms by which they interact beneficially with plants have only been poorly elucidated. A combination of features makes Azoarcus sp. strain BH72 an excellent model grassendophyte 4 . (i) It supplies nitrogen derived from N 2 fixation to its host, Kallar grass (Leptochloa fusca (L.) Kunth); in planta it is usually not culturable, but can be detected by culture-independent methods based on nifH-encoding nitrogenase reductase, the key enzyme for N 2 fixation 2 . (ii) It colonizes nondiseased plants in remarkably high numbers: estimates range from 10 8 cells (culturable cells per gram root dry weight (RDW) of field-grown Kallar grass 5 ) to 10 10 cells (estimated on the basis of abundance of bacterial nifH-mRNA in roots) 2 . (iii) It is the only cultured grass endophyte shown by molecular methods to be the most actively N 2 -fixing bacterium of the natural population in roots 2 . (iv) It also colonizes the roots of rice, a cereal of global importance, in high numbers (10 9 cells per g RDW) in the laboratory, and spreads systemically into shoots 6 . Plant stress response is only very limited in a compatible, that is, well-colonized rice cultivar 7 . Notably, Azoarcus sp. strain BH72 is capable of endophytic N 2 -fixation inside the roots of rice 8 .For a wider application in agriculture, more knowledge is required on mechanisms o...

Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501

“…(Table S3). A1501 should get iron from siderophores produced by other soil bacteria in the rhizosphere, a feature also reported in Azoarcus (13).…”

“…BH72 (13). The general organization of the nif genes in A1501 showed a high degree of similarity to that of A. vinelandii, except that the nif genes were not contiguous in A. vinelandii, but were distributed into two portions of the genome (Fig.…”

“…For example, the 10 genes from PST1349 (hesB-like gene) to PST1358 were likely to be part of the same 7.5-kb transcriptional unit, suggesting a superoperon with translational coupling. Although nitrogenase on-off switching was reported in A1501 (11), draT and draG genes known to control the nitrogenase ADP ribosylation process were not found in A1501, suggesting an inactivation mechanism different from that reported in Azoarcus and A. brasilense (12,13). Transcriptomic analysis of the whole A1501 genome was implemented by using genome-wide microarrays.…”

“…In addition to symbiotic nitrogen-fixing microorganisms, which induce differentiated structures on the host plant (root nodules of legumes and actinorhizal plants), there exist a variety of free-living nitrogen-fixing bacteria capable of association with the root system of graminaceous plants, such as Klebsiella pneumoniae, Azotobacter vinelandii, and Azospirillum brasilense (12). New species, such as Azoarcus and Gluconacetobacter, can also develop endophytic associations and survive within plant tissues without causing disease symptoms (12,13).…”

The periplasmic nitrate reductase in Shewanella: the resolution, distribution and functional implications of two NAP isoforms, NapEDABC and NapDAGHB

“…The presence of two nap operons on the genome of Azoarcus sp. BH72 has been noted previously (Krause et al, 2006). Therefore: (i) it is unusual for a bacterial genome to have more than one nap operon; and (ii) the presence of two nap operons in the genomes of most Shewanella species (observed in 16 of the 19 strains examined) is an unusual feature of this genus.…”