Arbuscular mycorrhizal (AM) fungi form tight symbiotic relationships with the majority of terrestrial plants and play critical roles in plant P acquisition, adding a further dimension of complexity. The plant-AM fungus-bacterium system is considered a continuum, with the bacteria colonizing not only the plant roots, but also the associated mycorrhizal hyphal network, known as the hyphosphere microbiome. Plant roots are usually colonized by different AM fungal species which form an independent phosphorus uptake pathway from the root pathway, i.e., the mycorrhizal pathway.

Understanding the mechanism of iron (Fe)‐deficiency responses is crucial for improving plant Fe bioavailability. Here, we found that the Arabidopsis Rho‐like GTPase 6 mutant (rop6) is less sensitive to Fe‐deficiency responses and has reduced levels of reactive oxygen species (ROS) compared to wild‐type (WT), while AtROP6‐overexpressing seedlings exhibit more sensitivity to Fe‐deficiency responses and has higher levels of ROS compared to WT. Moreover, treatment with H2O2 improves the sensitivity to Fe‐deficiency responses in rop6 mutants. By using the yeast two‐hybrid system, we further demonstrate the direct interaction between AtROP6 and Arabidopsis respiratory burst oxidase homolog D (AtRBOHD), which controls the generation of ROS. Overall, we suggest that AtROP6 is involved in AtRBOHD‐mediated ROS signaling to modulate Fe‐deficiency responses in Arabidopsis thaliana.

Nitrogen is critical for plant growth and development. With the increase of nitrogen fertilizer application, nitrogen use efficiency decreases, resulting in wasted resources. In apple (Malus domestica) rootstocks, the potential molecular mechanism for improving nitrogen uptake efficiency to alleviate low nitrogen stress remains unclear. We utilized multi-omics approaches to investigate the mechanism of nitrogen uptake in two apple rootstocks with different responses to nitrogen stress, Malus hupehensis and Malus sieversii. Under low nitrogen stress, Malus sieversii showed higher efficiency in nitrogen uptake. Multi-omics analysis revealed substantial differences in the expression of genes involved in flavonoid and lignin synthesis pathway between the two materials, which were related to the corresponding metabolites. We discovered that basic helix-loop-helix 130 (bHLH130) transcription factor was highly negatively associated with the flavonoid biosynthetic pathway. bHLH130 may directly bind to the chalcone synthase gene (CHS) promoter and inhibit its expression. Overexpressing CHS increased flavonoid accumulation and nitrogen uptake. Inhibiting bHLH130 increased flavonoid biosynthesis while decreasing lignin accumulation, thus improving nitrogen uptake efficiency. These findings revealed the molecular mechanism by which bHLH130 regulates flavonoid and lignin biosynthesis in apple rootstocks under low nitrogen stress.

Plants have developed complex mechanisms to adapt to the changing nitrate (NO3-) levels and can recruit microbes to boost nitrogen absorption. However, little is known about the relationship between functional genes and the rhizosphere microbiome in NO3- uptake of apple rootstocks. Here, we found that variation in MdNRT2.4 expression contributes to nitrate-uptake divergence between two apple rootstocks. Overexpression of MdNRT2.4 in apple seedlings significantly improved tolerance to low nitrogen via increasing net NO3- influx at root surface. But when inhibited the root plasma membrane H +-ATPase activity, which abolished NO3- uptake and led to NO3- release, suggesting that MdNRT2.4 encodes an H +-coupled nitrate transporter. Surprisingly, the nitrogen concentration of MdNRT2.4-overexpressing apple seedlings in unsterilized nitrogen-poor soil was higher than that in sterilized nitrogen-poor soil. Using 16S ribosomal RNA gene profiling to characterize rhizosphere microbiota, we found that MdNRT2.4-overexpressing apple seedlings recruited more bacterial taxa with nitrogen metabolic functions, especially Rhizobiaceae. We isolated a bacterial isolate AR11 from apple rhizosphere soil and identified it as Rhizobium. Inoculation with ARR11 improved apple seedling growth in nitrogen-poor soil compared with uninoculated seedlings. Together, our results highlight the interaction of host plant genes with the rhizosphere microbiota for host plant nutrient uptake.

Aims:To select apple rootstocks that are tolerant to low nitrogen and reveal the relationship between the rhizosphere bacterial communities and the low nitrogen tolerance of the apple rootstock. Methods and Results: In total, 235 lines of hybrids of Malus robusta Rehd. 9 M.9 with low nitrogen stress were cultivated in pots in a greenhouse equipped with a drip irrigation system, and growth characteristics, photosynthesis traits and mineral elements were monitored. The bacterial community structure of the rhizosphere from different rootstocks was determined via Illumina MiSeq sequencing. This study selected three low nitrogen-tolerant (NT) lines that had higher nitrogen concentration, and higher photosynthesis rate than the three low nitrogen-sensitive (NS) lines. The bacterial community structure significantly differed (P ≤ 0Á001) among the rootstocks. The bacterial phyla Proteobacteria and Actinobacteria were the dominant groups in the rhizosphere and presented higher abundance in the NT rhizosphere. The N concentration in the apple rootstocks exhibited highly positive Pearson correlations with the bacterial genera Sphingomonas, Pseudoxanthomonas, Bacillus and Acinetobacter, and negative correlations with the bacterial genera Pseudarthrobacter and Bradyrhizobium. Conclusions: This study showed that investigated rootstocks achieved increased nitrogen concentration by enhancing their photosynthetic production capacity and shaping their rhizobacteria community structure. Significance and Impact of the Study: The findings provide a basis for studying the mechanisms of resistance to low nitrogen stress in apple rootstocks. Based on these beneficial bacteria, microbial inoculants can be developed for use in sustainable agricultural and horticultural production. 60 days. For each line, three replicate samples were set.The nutrient solution contained 40 lmol l À1 Fe 3+ -EDTA, 3 lmol l À1 MnCl 2 , 0Á3 mmol l À1 Mg(NO 3 ) 2 Á6H 2 O, 0Á5 mmol l À1 KNO 3 , 0Á05 lmol l À1 H 2 MoO 4 ÁH 2 O, 0Á5 mmol l À1 Journal of Applied Microbiology 126, 595--607 © 2018 The Society for Applied Microbiology 596Bacteria in the apple rootstock rhizosphere X. Chai et al.

<p>Plant roots are usually colonized by various arbuscular mycorrhizal (AM) fungal species, which vary in morphological, physiological, and genetic traits. This colonization constitutes the mycorrhizal nutrient uptake pathway (MP) and supplements the pathway through roots. Simultaneously, the extraradical hyphae of each AM fungus is associated with a community of bacteria. However, whether the community structure and function of the microbiome on the extraradical hyphae differ between AM fungal species remains unknown. In order to understand the community structure and the predicted functions of the microbiome associated with different AM fungal species, a splitroot compartmented rhizobox cultivation system, which allowed us to inoculate two AM fungal species separately in two root compartments, was used. We inoculated two separate AM fungal species combinations, (i) F<em>unneliformis mosseae</em> and <em>Gigaspora margarita</em> and (ii) <em>Rhizophagus intraradices </em>and <em>G. margarita</em>, on a single root system of cotton. The hyphal exudate-fed, active microbiome was measured by combining <sup>13</sup>C-DNA stable isotope probing with MiSeq sequencing. We found that different AM fungal species, which were simultaneously colonizing a single root system, hosted active microbiomes that were distinct from one another. Moreover, the predicted potential functions of the different microbiomes were distinct. We conclude that the arbuscular mycorrhizal fungal component of the system is responsible for the recruitment of distinct microbiomes in the hyphosphere. We found that arbuscular mycorrhizal fungi cocolonizing on single plant roots recruit their own specific microbiomes, which should be considered in evaluating plant microbiome form and function. Our findings demonstrate the importance of understanding trophic interactions in order to gain insight into the plant-AM fungus-bacterium symbiosis</p>

Background: Plant roots are usually colonized by various arbuscular mycorrhizal (AM) fungal species which vary in morphological, physiological and genetic traits and constitute the mycorrhizal nutrient uptake pathway (MP) in addition to roots. Simultaneously, the extraradical hyphae of each AM fungus is associated with a community of bacteria. However, whether the community structure and function of microbiome on the extraradical hyphae would differ between the AM fungal species are mostly unknown. Methods: In order to understand the community structure and the predicted functions of the microbiome associated with different AM fungal species, a split-root compartmented rhizobox culturing system, which allowed us to inoculate two AM fungal species separately in two root compartments was used. We inoculated two separate AM fungal species combinations, Funneliformis mosseae ( F.m ) and Gigaspora margarita ( G.m ), Rhizophagus intraradices ( R.i ) and G. margarita, on a single root system of cotton . The hyphal exudate fed active microbiome was measured by combining 13 C-DNA stable isotope probing with Miseq sequencing. Results: We found different AM fungal species, that were simultaneously colonizing on a single root system, hosted distinct active microbiomes from one another. Moreover, the predicted potential functions of the different microbiomes were distinct. Conclusion: We conclude that the arbuscular mycorrhizal fungi component of the system is responsible for the recruitment distinct microbiomes in the hyphosphere. The potential significance of the predicted functions of the microbiome ecosystem services is discussed.

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