BackgroundAll plants in nature harbor a diverse community of endophytic bacteria which can positively affect host plant growth. Changes in plant growth frequently reflect alterations in phytohormone homoeostasis by plant-growth-promoting (PGP) rhizobacteria which can decrease ethylene (ET) levels enzymatically by 1-aminocyclopropane-1-carboxylate (ACC) deaminase or produce indole acetic acid (IAA). Whether these common PGP mechanisms work similarly for different plant species has not been rigorously tested.Methodology/ Principal FindingsWe isolated bacterial endophytes from field-grown Solanum nigrum; characterized PGP traits (ACC deaminase activity, IAA production, phosphate solubilization and seedling colonization); and determined their effects on their host, S. nigrum, as well as on another Solanaceous native plant, Nicotiana attenuata. In S. nigrum, a majority of isolates that promoted root growth were associated with ACC deaminase activity and IAA production. However, in N. attenuata, IAA but not ACC deaminase activity was associated with root growth. Inoculating N. attenuata and S. nigrum with known PGP bacteria from a culture collection (DSMZ) reinforced the conclusion that the PGP effects are not highly conserved.Conclusions/ SignificanceWe conclude that natural endophytic bacteria with PGP traits do not have general and predictable effects on the growth and fitness of all host plants, although the underlying mechanisms are conserved.

Summary• A plant's bacterial endophyte community is thought to be recruited from the rhizosphere, but how this recruitment is influenced by the plant's phytohormone signaling is unknown. Ethylene regulates plant-microbe interactions; here, we assess the role of ethylene in the recruitment of culturable endophytic bacteria from native soils.• We grew wild-type Nicotiana attenuata plants and isogenic transformed plants deficient in ethylene biosynthesis (ir-aco1) or perception (35S-etr1) in four native soils and quantified the extent of culturable bacterial endophyte colonization (by plate counting) and diversity (by amplified rDNA restriction analysis and 16S rDNA sequencing).• The endophyte community composition was influenced by soil type and ethylene signaling. Plants grown in organic (vs mineral) soils harbored a more diverse community and plants impaired in ethylene homeostasis harbored a less diverse community than wild-type plants. Wild-type and ethylene signaling-impaired plants fostered distinct bacteria in addition to common ones. In vitro re-colonization by common and genotype-specific isolates demonstrated the specificity of some associations and the susceptibility of 35S-etr1 seedlings to all tested bacterial isolates, suggesting an active process of colonization driven by plant-and microbespecific genes.• We propose that soil composition and ethylene homeostasis play central roles in structuring the bacterial endophyte community in N. attenuata roots.

SUMMARYUsing a proteomics approach, a PP2C-type phosphatase (renamed PIA1, for PP2C induced by AvrRpm1) was identified that accumulates following infection by Pseudomonas syringae expressing the type III effector AvrRpm1, and subsequent activation of the corresponding plant NB-LRR disease resistance protein RPM1. No accumulation of PIA1 protein was seen following infection with P. syringae expressing AvrB, another type III effector that also activates RPM1, although PIA transcripts were observed. Accordingly, mutation of PIA1 resulted in enhanced RPM1 function in response to P. syringae pathover tomato (Pto) DC3000 (avrRpm1) but not to Pto DC3000 (avrB). Thus, PIA1 is a protein marker that distinguishes AvrRpm1-and AvrB-dependent activation of RPM1. AvrRpm1-induced expression of the pathogenesis-related genes PR1, PR2 and PR3, and salicylic acid accumulation were reduced in two pia1 mutants. By contrast, expression of other defense-related genes, including PR5 and PDF1.2 (plant defensin), was elevated in unchallenged pia1 mutants. Hence, PIA1 is required for AvrRpm1-induced responses, and confers dual (both positive and negative) regulation of defense gene expression.

Many plants have intimate relationships with soil microbes, which improve the plant’s growth and fitness through a variety of mechanisms. Bacillus sp. isolates are natural root-associated bacteria, isolated from Nicotiana attenuata plant roots growing in native soils. A particular isolate B55, was found to have dramatic plant growth promotion (PGP) effects on wild type (WT) and transgenic plants impaired in ethylene (ET) perception (35S-etr1), the genotype from which this bacterium was first isolated. B55 not only improves N. attenuata growth under in vitro, glasshouse, and field conditions, but it also “rescues” many of the deleterious phenotypes associated with ET insensitivity. Most notably, B55 dramatically increases the growth and survival of 35S-etr1 plants under field conditions. To our knowledge, this is the first demonstration of a PGP effect in a native plant–microbe association under natural conditions. Our study demonstrates that this facultative mutualistic plant–microbe interaction should be viewed as part of the plant’s extended phenotype. Possible modalities of recruitment and mechanisms of PGP are discussed.

A total of 239 isolates of blast (Pyricularia oryzae Cavara) collected from northern and central Vietnam showed a wide variation in pathogenicity based on the reaction patterns to 25 differential varieties (DVs) harboring 23 resistance genes and susceptible cultivar Lijiangxintuanheigu (LTH). The frequencies of isolates virulent toward DVs for Pish, Pik-m, Pi1, Pik-h, Pik, Pik-p, Pi7(t), Pi9(t), Piz-5, Pita-2, and Pita were low, but they were high for DVs for Pib, Pit, Pia, Pii, Pi3, Pi5(t), Pik-s, Piz, Piz-t, Pi12(t), Pi19(t), and Pi20(t). Isolates were classified into three cluster groups Ia, Ib, and II based on reaction patterns to DVs and LTH. The frequencies of isolates virulent toward 11 DVs for Pik-m, Pi1, Pik-h, Pik, Pik-p, Pi7(t), Pi9(t), Piz, Piz-5, Pita-2, and Pita in cluster II and DV for Piz-t were higher and lower than those of Ia and Ib, respectively. The frequencies to DVs for Pii, Pi3, Pi5(t), and Piz-t were different between clusters Ia and Ib. Clusters Ia and Ib were distributed with similar frequencies in the northeast, north central, and south central coast regions, but the frequencies among three cluster groups in the Red River Delta and northwest regions were different. This means that the blast races in these two regions were different from the others. Overall, the blast isolates were categorized into 153 races. Among them, 26 were selected as a set of standard differential blast isolates for characterizing 23 resistance genes and developing a differential system in Vietnam.