The structure of the culturable root bacterial endophyte community of Nicotiana attenuata is organized by soil composition and host plant ethylene production and perception.

*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 microbe-specific genes. *We propose that soil composition and ethylene homeostasis play central roles in structuring the bacterial endophyte community in N. attenuata roots.

A protein phosphatase 2C, responsive to the bacterial effector AvrRpm1 but not to the AvrB effector, regulates defense responses in Arabidopsis.

Using 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.

Native bacterial endophytes promote host growth in a species-specific manner; phytohormone manipulations do not result in common growth responses.

BACKGROUND: All 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 FINDINGS: We 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/SIGNIFICANCE: We 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.