Microbes of the phytomicrobiome are associated with every plant tissue and, in combination with the plant form the holobiont. Plants regulate the composition and activity of their associated bacterial community carefully. These microbes provide a wide range of services and benefits to the plant; in return, the plant provides the microbial community with reduced carbon and other metabolites. Soils are generally a moist environment, rich in reduced carbon which supports extensive soil microbial communities. The rhizomicrobiome is of great importance to agriculture owing to the rich diversity of root exudates and plant cell debris that attract diverse and unique patterns of microbial colonization. Microbes of the rhizomicrobiome play key roles in nutrient acquisition and assimilation, improved soil texture, secreting, and modulating extracellular molecules such as hormones, secondary metabolites, antibiotics, and various signal compounds, all leading to enhancement of plant growth. The microbes and compounds they secrete constitute valuable biostimulants and play pivotal roles in modulating plant stress responses. Research has demonstrated that inoculating plants with plant-growth promoting rhizobacteria (PGPR) or treating plants with microbe-to-plant signal compounds can be an effective strategy to stimulate crop growth. Furthermore, these strategies can improve crop tolerance for the abiotic stresses (e.g., drought, heat, and salinity) likely to become more frequent as climate change conditions continue to develop. This discovery has resulted in multifunctional PGPR-based formulations for commercial agriculture, to minimize the use of synthetic fertilizers and agrochemicals. This review is an update about the role of PGPR in agriculture, from their collection to commercialization as low-cost commercial agricultural inputs. First, we introduce the concept and role of the phytomicrobiome and the agricultural context underlying food security in the 21st century. Next, mechanisms of plant growth promotion by PGPR are discussed, including signal exchange between plant roots and PGPR and how these relationships modulate plant abiotic stress responses via induced systemic resistance. On the application side, strategies are discussed to improve rhizosphere colonization by PGPR inoculants. The final sections of the paper describe the applications of PGPR in 21st century agriculture and the roadmap to commercialization of a PGPR-based technology.

The ileal lipid binding protein (ilbp) is a cytoplasmic protein that binds bile acids with high affinity. However evidence demonstrating the role of this protein in bile acid transport and homeostasis is missing. We created a mouse strain lacking ilbp (Fabp6−/− mice) and assessed the impact of ilbp deficiency on bile acid homeostasis and transport in vivo. Elimination of ilbp increased fecal bile acid excretion (54.2%, P<0.05) in female but not male Fabp6−/− mice. The activity of cholesterol 7α-hydroxylase (cyp7a1), the rate-controlling enzyme of the classical bile acid biosynthetic pathway, was significantly increased in female (63.5%, P<0.05) but not in male Fabp6−/− mice. The amount of [3H]taurocholic acid (TCA) excreted by 24 h after oral administration was 102% (P<0.025) higher for female Fabp6−/− mice whereas it was 57.3% (P<0.01) lower for male Fabp6−/− mice, compared to wild-type mice. The retained fraction of the [3H]TCA localized in the small and large intestines was increased by 22% (P<0.02) and decreased by 62.7% (P<0.01), respectively, in male Fabp6−/− mice relative wild-type mice, whereas no changes were seen in female Fabp6−/− mice. Mucosal to serosal bile acid transport using everted distal gut sacs was decreased by 74% (P<0.03) in both sexes of Fabp6−/− mice as compared to wild-type mice. The results demonstrate that ilbp is involved in the apical to basolateral transport of bile acids in ileal enterocytes, and is vital for the maintenance of bile acid homeostasis in the enterohepatic circulation (EHC) in mice.

The organisms of the phytomicrobiome use signal compounds to regulate aspects of each other’s behavior. Legumes use signals (flavonoids) to regulate rhizobial nod gene expression during establishment of the legume-rhizobia N2-fixation symbiosis. Lipochitooligosaccharides (LCOs) produced by rhizobia act as return signals to the host plant and are recognized by specific lysine motif receptor like kinases, which triggers a signal cascade leading to nodulation of legume roots. LCOs also enhance plant growth, particularly when plants are stressed. Chitooligosaccharides activate plant immune responses, providing enhanced resistance against diseases. Co-inoculation of rhizobia with other plant growth promoting rhizobacteria (PGPR) can improve nodulation and crop growth. PGPR also alleviate plant stress by secreting signal compounds including phytohormones and antibiotics. Thuricin 17, a small bacteriocin produced by a phytomicrobiome member promotes plant growth. Lumichrome synthesized by soil rhizobacteria function as stress-sensing cues. Inter-organismal signaling can be used to manage/engineer the phytomicrobiome to enhance crop productivity, particularly in the face of stress. Stressful conditions are likely to become more frequent and more severe because of climate change.

The fatty acid binding protein 6 (Fabp6) is commonly regarded as a bile acid binding protein found in the distal portion of the small intestine and has been shown to be important in maintaining bile acid homeostasis. Previous studies have also reported the presence of Fabp6 in human, rat and fish ovaries, but the significance of Fabp6 in this organ is largely unknown. Therefore, we surveyed murine ovaries for Fabp6 gene expression and evaluated its role in ovarian function using mice with whole body Fabp6 deficiency. Here we show that the Fabp6 gene is expressed in granulosa and luteal cells of the mouse ovary. Treatment with gonadotropins stimulated Fabp6 gene expression in large antral follicles. The ovulation rate in response to superovulatory treatment in Fabp6-deficient mice was markedly decreased compared to wildtype (C57BL/6) mice. The results of this study suggest that expression of Fabp6 gene in granulosa cells serves an important and previously unrecognized function in fertility.

Sequence analysis of 4,230 bp of the 3' end of the ornithine decarboxylase gene of 20 chickens from a noninbred White Leghorn strain revealed a total of 62 polymorphisms. Of these 61% were transitions, 24% were transversions, and 16% were deletions or insertions. Despite the high number of polymorphisms, only 3 haplotypes were present among the 40 alleles analyzed. Based on the genetic distances between haplotypes they segregated early during domestication of the chicken. Ornithine decarboxylase is a pivotal enzyme in regulating the synthesis of polyamines, cations that are important regulators of cell division, differentiation, and apoptosis. Variants of ornithine decarboxylase are, therefore, expected to affect many different traits. Association analyses between genotypes and the major egg production traits in female chickens of the same strain revealed significant effects on the onset of sexual maturity, BW at sexual maturity, eggshell thickness (a measure of calcium deposition), and residual feed consumption (a measure of the metabolic rate). Further, comparisons of the genotypes indicated that the 3 haplotypes differ in their phenotypic properties. Our results show that variations in a gene that is ubiquitously expressed in all cells of an organism may nevertheless contribute to distinct phenotypic properties of the organism as a whole.

Vitamin D is an important immunomodulator that mediates its effect via a nuclear receptor. In this study, we analyzed 3 uncorrelated genetic markers (tag single nucleotide polymorphisms) in the vitamin D receptor gene for association with Marek's disease (MD) resistance. The database consisted of 400 commercial White Leghorn chickens that had been vaccinated with herpes turkey virus and challenged by intraperitoneal injection of the virulent MD virus RB1B. Viral titers in feather tips were determined at weekly intervals for 8 wk, mortality was recorded, and necropsy analyses preformed on all chickens. The 3 genotypes defined by 1 of the markers were associated with significant differences in the viral load (integration of the viral titer over time; P = 3 x 10(-4)). The effect was additive, with the 2 homozygotes differing by a factor of 2. The ranking of the genotypes by viral load, frequency of MD lesions, mortality, and bursal atrophy were consistent. There was no effect on the tissue distribution of MD lesions. The degree of MD resistance in the 9 genotypes defined by the 3 tag single nucleotide polymorphisms was proportional to the frequency of major histocompatibility complex class II-positive peripheral blood leukocytes that had been previously measured in uninfected chickens in a different database.

A total of 114 male chickens from three sire families of a commercial cross of White Leghorn chickens were infected with RB-1B Marek's disease (MD) virus at 21 days of age by exposing them to chickens previously inoculated with MD virus. The presence of virus in feather tips, feather pulp, and MD viral antibodies indicated all chickens became infected. The first virus-positive chickens were observed at 12 days postexposure (dpe). The frequency reached a maximum at 27 dpe and then decreased. At 80 dpe, when the experiment was terminated, no viral DNA was detected in the feather pulp of the surviving chickens (82%). Death from MD was first observed at 38 dpe and reached 18% by the end of the experiment, with spleen lesions being the major MD lesion. The viral genome titers in spleen extracts of chickens with MD lesions was negatively correlated with the time of death, and, similar to feather pulp, none of the surviving chickens was virus positive at the end of the experiment. Quantization of the viral genome titers in feather tip extracts at 27 and 38 dpe revealed a positive correlation with the presence of MD lesions, but only in the declining phase (38 dpe) and not at the peak (27 dpe) of the viral titer. Sire effects were significant, indicating the presence of genetic factors that affect viral proliferation. Again, significance was only observed at 38 dpe and not at 27 dpe. The results indicate that, in this commercial line, 1) all chickens were susceptible to infection via contact exposure, 2) all surviving chickens recovered from the viral infection, and 3) it is not sufficient to measure viral titers at a single time point when using viral titers as an endpoint for MD susceptibility.