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Summary: Legumes such as soybean are considered important crops as they provide proteins and oils for humans and livestock around the world. Different from other crops, leguminous crops accumulate nitrogen (N) for plant growth through symbiotic nitrogen fixation (SNF) in coordination with rhizobia. A number of studies have shown that efficient SNF requires the cooperation of other nutrients, especially phosphorus (P), a nutrient deficient in most soils. During the last decades, great progress has been made in understanding the molecular mechanisms underlying the interactions between SNF and P nutrition, specifically through the identification of transporters involved in P transport to nodules and bacteroids, signal transduction, and regulation of P homeostasis in nodules. These studies revealed a distinct N–P interaction in leguminous crops, which is characterized by specific signaling cross talk between P and SNF. This review aimed to present an updated picture of the cross talk between N fixation and P nutrition in legumes, focusing on soybean as a model crop, and Medicago truncatula and Lotus japonicus as model plants. We also discuss the possibilities for enhancing SNF through improving P nutrition, which are important for high and sustainable production of leguminous crops. [ABSTRACT FROM AUTHOR]

Rhizosphere bacterial communities are vital for plants, yet the composition of rhizobacterial communities and the complex interactions between roots and microbiota, or between microbiota, are largely unknown. In this study, we investigated the structure and composition of rhizobacterial communities in two soybean cultivars and their recombinant inbred lines contrasting in nodulation through 16S rRNA amplicon sequencing in two years of field trials. Our results demonstrate that soybean plants are able to select microbes from bulk soils at the taxonomic and functional level. Soybean genotype significantly influenced the structure of rhizobacterial communities and resulted in dramatically different co‐occurrence networks of rhizobacterial communities between different genotypes of soybean plants. Furthermore, the introduction of exogenous rhizobia through inoculation altered soybean rhizobacterial communities in genotype‐dependent manner. Rhizobium inoculation not only stimulated the proliferation of potential beneficial microbes but also increased connections in rhizobacterial networks and changed the hub microbes, all of which led to the association of distinctive bacterial communities. Taken together, we demonstrated that the assembly of soybean rhizobacterial communities was determined by both genotype and the introduction of exogenous rhizobia. These findings bolster the feasibility of root microbiome engineering through inoculation of specific microbial constituents. Rhizosphere bacterial communities are vital for plant growth and development. In this study, we demonstrate that soybean plants display taxonomic and functional selection on microbes from bulk soils. Besides, both soybean genotype and exogenous rhizobia through inoculation significantly influence the structure of rhizobacterial communities. These findings bolster the feasibility of root microbiome engineering through inoculation of specific microbial constituents. [ABSTRACT FROM AUTHOR]

Summary: Phosphorus (P) is an essential macronutrient for plant growth and development, but the molecular mechanism determining how plants sense external inorganic phosphate (Pi) levels and reprogram transcriptional and adaptive responses is incompletely understood. In this study, we investigated the function of OsSPX6 (hereafter SPX6), an uncharacterized member of SPX domain (SYG1, Pho81 and XPR1)‐containing proteins in rice, using reverse genetics and biochemical approaches. Transgenic plants overexpressing SPX6 exhibited decreased Pi concentrations and suppression of phosphate starvation‐induced (PSI) genes. By contrast, transgenic lines with decreased SPX6 transcript levels or spx6 mutant showed significant Pi accumulation in the leaf and upregulation of PSI genes. Overexpression of SPX6 genetically suppressed the overexpression of PHOSPHATE STARVATION RESPONSE REGULATOR 2 (PHR2) in terms of the accumulation of high Pi content. Moreover, direct interaction of SPX6 with PHR2 impeded PHR2 translocation into the nucleus, and inhibited PHR2 binding to the P1BS (PHR1 binding sequence) element. SPX6 protein was degraded in leaves under Pi‐deficient conditions, whereas it accumulated in roots. We conclude that rice SPX6 is another important negative regulator in Pi starvation signaling through the interaction with PHR2. SPX6 shows different responses to Pi starvation in shoot and root, which differ from those of other SPX proteins. [ABSTRACT FROM AUTHOR]

PHR2, a central regulator of phosphate signaling in rice, enhanced the expression of phosphate starvation-induced (PSI) genes and resulted in the enhancement of Pi acquisition under Pi deficiency stress. This occurred via PHR2 binding to a cis -element named the PHR1 binding sequences. However, the transcription level of PHR2 was not responsive to Pi starvation. So how is activity of transcription factor PHR2 adjusted to adapt diverse Pi status? Here, we identify an SPX family protein, Os-SPX4 (SPX4 hereafter), involving in Pi starvation signaling and acting as a negative regulator of PHR2. SPX4 is shown to be a fast turnover protein. When Pi is sufficient, through its interaction with PHR2, SPX4 inhibits the binding of PHR2 to its cis -element and reduces the targeting of PHR2 to the nucleus. However, when plants grow under Pi deficiency, the degradation of SPX4 is accelerated through the 26S proteasome pathway, thereby releasing PHR2 into the nucleus and activating the expression of PSI genes. Because the level of SPX4 is responsive to Pi concentration and SPX4 interacts with PHR2 and regulates its activity, this suggests that SPX4 senses the internal Pi concentration under diverse Pi conditions and regulates appropriate responses to maintain Pi homeostasis in plants. [ABSTRACT FROM AUTHOR]

Rhizobacteria is an important ingredient for growth and health of medicinal herbs, and synthesis of pharmacological effective substances from it. In this study, we investigated the community structure and composition of rhizobacteria in Baphicacanthus cusia (NeeS) Bremek via 16S rRNA amplicon sequencing. We obtained an average of 3,371 and 3,730 OTUs for bulk soil and rhizosphere soil samples respectively. Beta diversity analysis suggested that the bacterial community in the rhizosphere was distinctive from that in the bulk soil, which indicates that B.cusia can specifically recruit microbes from bulk soil and host in the rhizosphere. Burkholderia was significantly enriched in the rhizosphere. Burkholderia is a potentially beneficial bacteria that has been reported to play a major role in the synthesis of indigo, which was a major effective substances in B. cusia. In addition, we found that Bacilli were depleted in the rhizosphere, which are useful for biocontrol of soil-borne diseases, and this may explain the continuous cropping obstacles in B. cusia. Our results revealed the structure and composition of bacterial diversity in B. cusia rhizosphere, and provided clues for improving the medicinal value of B. cusia in the future. [ABSTRACT FROM AUTHOR]

Soybean (Glycine max (L.) Merr.) is an important nutritional crop with high seed protein content. Production of high protein concentrations relies on sufficient nutrient supplies, especially of nitrogen (N) and phosphorus (P). Although the genetic basis for seed quality traits has been well studied, little information exists on any genetic connections between seed quality and nutrient supplies in soybean. Here, a recombinant inbred line (RIL) population of 179 progeny was generated using HC6 and JD17 as parents contrasting in seed quality and N and P translocation efficiencies. Seed protein and N and P translocation efficiencies were higher in HC6 than in JD17. Meanwhile, positive correlations were observed between seed protein content and translocation efficiency of N and P in RILs, implying that high N and P translocation efficiencies might facilitate seed protein accumulation. A genetic map was constructed using 5250 SNP markers covering a genetic distance of 3154.83 cM. A total of 6 loci for quality and 13 loci for N and P translocation efficiency were detected. Among them, two fragments on chromosome 6 and chromosome 20 contained multiple significant markers for both quality and N and P translocation efficiencies, with the respective observed LOD values ranging from 2.98 to 5.61, and 3.01 to 11.91, while the respective PVE values ranged from 8.2% to 13.9%, and 8.3% to 28.0%. Interestingly, one significant locus on chromosome 20 appears to be the product of a transposable element (TE) InDel in Glyma.20G085100, with progeny lacking the TE also exhibiting higher N and P translocation efficiencies, along with higher seed protein contents. Taken together, these results provide genetic evidence that increasing N and P translocation efficiencies may lead to increasing protein contents in soybean seeds. Furthermore, a TE InDel may be used as a genetic marker for breeding elite soybean cultivars with high protein content and N and P translocation efficiencies. [ABSTRACT FROM AUTHOR]

MYB-CC transcription factors (TFs) are essential for plant growth and development. Members of the MYB-CC subfamily with long N terminal domains, such as phosphate starvation response 1 (PHR1) or PHR1-like TFs, have well documented functions, while those with short N terminal domains remain less understood. In this study, we identified a nodule specific MYB-CC transcription factor 1 (GmPHR1) in soybean that is different from other canonical PHR family genes in that GmPHR1 harbors a short N terminal ahead of its MYB-CC domain and was highly induced by rhizobium infection. The overexpression of GmPHR1 dramatically increased the ratio of deformed root hairs, enhanced subsequent soybean nodulation, and promoted soybean growth in pot experiments. The growth promotion effects of GmPHR1 overexpression were further demonstrated in field trails in which two GmPHR1-OE lines yielded 10.78% and 8.19% more than the wild type line. Transcriptome analysis suggested that GmPHR1 overexpression led to global reprogramming, with 749 genes upregulated and 279 genes downregulated, especially for genes involved in MYB transcription factor activities, root growth, and nutrient acquisition. Taken together, we conclude that GmPHR1 is a key gene involved in the global regulation of nodulation, root growth, and nutrient acquisition in soybeans, and is thus a promising candidate gene to target for soybean yield enhancement. [ABSTRACT FROM AUTHOR]

Symbiotic nitrogen fixation (SNF) provides sufficient nitrogen (N) to meet most legume nutrition demands. In return, host plants feed symbionts carbohydrates produced in shoots. However, the molecular dialogue between shoots and symbionts remains largely mysterious. Here, we report the map-based cloning and characterization of a natural variation in GmNN1, the ortholog of Arabidopsis thaliana FLOWERING LOCUS T (FT2a) that simultaneously triggers nodulation in soybean and modulates leaf N nutrition. A 43-bp insertion in the promoter region of GmNN1/FT2a significantly decreased its transcription level and yielded N deficiency phenotypes. Manipulating GmNN1/GmFT2a significantly enhanced soybean nodulation, plant growth, and N nutrition. The near-isogenic lines (NILs) carrying low mRNA abundance alleles of GmNN1/FT2a, along with stable transgenic soybeans with CRISPR/Cas9 knockouts of GmNN1/FT2a, had yellower leaves, lower N concentrations, and fewer nodules than wild-type control plants. Grafting together with split-root experiments demonstrated that only shoot GmNN1/FT2a was responsible for regulating nodulation and thereby N nutrition through shoot-to-root translocation, and this process depends on rhizobial infection. After translocating into roots, shoot-derived GmNN1/FT2a was found to interact with GmNFYA-C (nuclear factor-Y subunit A-C) to activate symbiotic signaling through the previously reported GmNFYA-C-ENOD40 module. In short, the description of the critical soybean nodulation regulatory pathway outlined herein sheds novel insights into the shoot-to-root signaling required for communications between host plants and root nodulating symbionts. Symbiotic nitrogen fixation provides a vital nitrogen source in agroecosystems but nodulation is tightly controlled by a long-distance signaling system. This study uses map-based cloning to reveal GmNN1/FT2a as a new shoot-to-root mobile protein that significantly regulates nodule formation and thus nitrogen nutrition in soybean. [ABSTRACT FROM AUTHOR]

Root‐associated microbes are critical for plant growth and nutrient acquisition. However, scant information exists on optimizing communities of beneficial root‐associated microbes or the mechanisms underlying their interactions with host plants. In this report, we demonstrate that root‐associated microbes are critical influencers of host plant growth and nutrient acquisition. Three synthetic communities (SynComs) were constructed based on functional screening of 1,893 microbial strains isolated from root‐associated compartments of soybean plants. Functional assemblage of SynComs promoted significant plant growth and nutrient acquisition under both N/P nutrient deficiency and sufficiency conditions. Field trials further revealed that application of SynComs stably and significantly promoted plant growth, facilitated N and P acquisition, and subsequently increased soybean yield. Among the tested communities, SynCom1 exhibited the greatest promotion effect, with yield increases of up to 36.1% observed in two field sites. Further RNA‐seq implied that SynCom application systemically regulates N and P signaling networks at the transcriptional level, which leads to increased representation of important growth pathways, especially those related to auxin responses. Overall, this study details a promising strategy for constructing SynComs based on functional screening, which are capable of enhancing nutrient acquisition and crop yield through the activities of beneficial root‐associated microbes. [ABSTRACT FROM AUTHOR]

Summary: Legume crops contribute a great portion of clean nitrogen (N) to agro‐ecosystems through symbiotic N2 fixation in the nodule; however, the nodulation is always inhibited by high N availability which is known as the N inhibitory effect through largely unknown mechanisms.We functionally investigated miR169c‐GmNFYA‐C‐GmENOD40 under multiple N conditions in soybean (Glycine max) (ENOD, Early Nodulin; NFYA, Nuclear Factor‐Y Subunit A). We elucidated their regulatory roles in soybean nodulation through analyzing expression patterns, micro–messenger RNA (miRNA–mRNA) interactions, phenotypes of transgenic soybean plants and genetic interactions.We found that miR169c expression was induced by high N, whereas its target GmNFYA‐C was preferentially expressed in nodules and induced by rhizobium inoculation. Overexpression of miR169c inhibited nodulation through targeting 3′‐UTR of GmNFYA‐C, whereas knockout miR169c through CRISPR‐cas9 promoted nodulation. However, overexpression of GmNFYA‐C promoted soybean nodulation through facilitating rhizobium infection and increasing the expression of symbiotic signaling gene GmENOD40. Besides, GmNFYA‐C directly induced the expression of GmENOD40. In addition, overexpression of GmNFYA‐C without the target site of miR169c partially attenuated the inhibitory effect of high N on soybean nodulation.We discovered a new regulatory pathway involving the miR169c‐NFYA‐C‐ENOD40 module that regulates soybean nodulation in response to N availability. This pathway provides substantial new insights into the mechanisms underlying the N inhibitory effect on nodulation. [ABSTRACT FROM AUTHOR]

Background: Low temperature is a major abiotic stress that seriously limits mangrove productivity and distribution. Kandelia obovata is the most cold-resistance specie in mangrove plants, but little is known about the molecular mechanism underlying its resistance to cold. Osmotin is a key protein associated with abiotic and biotic stress response in plants but no information about this gene in K. obovata was reported. Results: In this study, a cDNA sequence encoding osmotin, KoOsmotin (GenBank accession no. KP267758), was cloned from mangrove plant K. obovata. The KoOsmotin protein was composed of 221 amino acids and showed a calculated molecular mass of 24.11 kDa with pI 4.92. The KoOsmotin contained sixteen cysteine residues and an N-terminal signal peptide, which were common signatures to most osmotins and pathogenesis-related 5 proteins. The three-dimensional (3D) model of KoOsmotin, contained one α-helix and eleven β-strands, was formed by three characteristic domains. Database comparisons of the KoOsmotin showed the closest identity (55.75%) with the osmotin 34 from Theobroma cacao. The phylogenetic tree also revealed that the KoOsmotin was clustered in the branch of osmotin/OLP (osmotin-like protien). The KoOsmotin protein was proved to be localized to both the plasma membrane and cytoplasm by the subcellular localization analysis. Gene expression showed that the KoOsmotin was induced primarily and highly in the leaves of K. obovata, but less abundantly in stems and roots. The overexpressing of KoOsmotin conferred cold tolerance in Escherichia coli cells. Conclusion: As we known, this is the first study to explore the osmotin of K. obovata. Our study provided valuable clues for further exploring the function of KoOsmotin response to stress. [ABSTRACT FROM AUTHOR]

Symbiotic nitrogen fixation (SNF) provides much of the N utilized by leguminous plants throughout growth and development. Legumes may simultaneously establish symbiosis with different taxa of microbial symbionts. Yet, the mechanisms used to steer associations toward symbionts that are most propitious across variations in soil types remain mysterious. Here, we demonstrate that GmRj2/Rfg1 is responsible for regulating symbiosis with multiple taxa of soybean symbionts. In our experiments, the GmRj2/Rfg1 SC haplotype favored association with Bradyrhizobia , which is mostly distributed in acid soils, whereas the GmRj2/Rfg1 HH haplotype and knockout mutants of GmRj2/Rfg1 SC associated equally with Bradyrhizobia and Sinorhizobium. Association between GmRj2/Rfg1 and NopP, furthermore, appeared to be involved in symbiont selection. Furthermore, geographic distribution analysis of 1,821 soybean accessions showed that GmRj2/Rfg1 SC haplotypes were enriched in acidic soils where Bradyrhizobia were the dominant symbionts, whereas GmRj2/Rfg1 HH haplotypes were most prevalent in alkaline soils dominated by Sinorhizobium , and neutral soils harbored no apparent predilections toward either haplotype. Taken together, our results suggest that GmRj2/Rfg1 regulates symbiosis with different symbionts and is a strong determinant of soybean adaptability across soil regions. As a consequence, the manipulation of the GmRj2/Rfg1 genotype or application of suitable symbionts according to the haplotype at the GmRj2/Rfg1 locus might be suitable strategies to explore for increasing soybean yield through the management of SNF. [Display omitted] • GmRj2 / Rfg1 determines the taxa of symbionts selected by soybean • Variations in GmRj2/Rfg1 confer better adaptation of soybean in various soil types • Associations between GmRj2/Rfg1 and NopP might be determinant in symbiont selection Li et al. provide new insights into genome-based symbiont selection in soybean, which confers better adaptation to various soil types by regulating the association with different symbionts. This study provides valuable information for soybean breeding programs incorporating beneficial microbes into agriculture management strategies. [ABSTRACT FROM AUTHOR]

Soybean (Glycine max L.) is a major crop providing important source for protein and oil for human life. Low phosphate (LP) availability is a critical limiting factor affecting soybean production. Soybean plants develop a series of strategies to adapt to phosphate (Pi) limitation condition. However, the underlying molecular mechanisms responsible for LP stress response remain largely unknown. Here, we performed a label-free quantification (LFQ) analysis of soybean leaves grown under low and high phosphate conditions. We identified 267 induced and 440 reduced differential proteins from phosphate-starved leaves. Almost a quarter of the LP decreased proteins are involved in translation processes, while the LP increased proteins are accumulated in chlorophyll biosynthetic and carbon metabolic processes. Among these induced proteins, an enolase protein, GmENO2a was found to be mostly induced protein. On the transcriptional level, GmENO2a and GmENO2b, but not GmENO2c or GmENO2d, were dramatically induced by phosphate starvation. Among 14 enolase genes, only GmENO2a and GmENO2b genes contain the P1BS motif in their promoter regions. Furthermore, GmENO2b was specifically induced in the GmPHR31 overexpressing soybean plants. Our findings provide molecular insights into how soybean plants tune basic carbon metabolic pathway to adapt to Pi deprivation through the ENO2 enzymes. [ABSTRACT FROM AUTHOR]