Under natural conditions, plants are always associated with a well-orchestrated community of microbes—the phytomicrobiome. The nature and degree of microbial effect on the plant host can be positive, neutral, or negative, and depends largely on the environment. The phytomicrobiome is integral for plant growth and function; microbes play a key role in plant nutrient acquisition, biotic and abiotic stress management, physiology regulation through microbe-to-plant signals, and growth regulation via the production of phytohormones. Relationships between the plant and phytomicrobiome members vary in intimacy, ranging from casual associations between roots and the rhizosphere microbial community, to endophytes that live between plant cells, to the endosymbiosis of microbes by the plant cell resulting in mitochondria and chloroplasts. If we consider these key organelles to also be members of the phytomicrobiome, how do we distinguish between the two? If we accept the mitochondria and chloroplasts as both members of the phytomicrobiome and the plant (entrained microbes), the influence of microbes on the evolution of plants becomes so profound that without microbes, the concept of the “plant” is not viable. This paper argues that the holobiont concept should take greater precedence in the plant sciences when referring to a host and its associated microbial community. The inclusivity of this concept accounts for the ambiguous nature of the entrained microbes and the wide range of functions played by the phytomicrobiome in plant holobiont homeostasis.

Terrestrial plants evolution occurred in the presence of microbes, the phytomicrobiome. The rhizosphere microbial community is the most abundant and diverse subset of the phytomicrobiome and can include both beneficial and parasitic/pathogenic microbes. Prokaryotes of the phytomicrobiome have evolved relationships with plants that range from non-dependent interactions to dependent endosymbionts. The most extreme endosymbiotic examples are the chloroplasts and mitochondria, which have become organelles and integral parts of the plant, leading to some similarity in DNA sequence between plant tissues and cyanobacteria, the prokaryotic symbiont of ancestral plants. Microbes were associated with the precursors of land plants, green algae, and helped algae transition from aquatic to terrestrial environments. In the terrestrial setting the phytomicrobiome contributes to plant growth and development by (1) establishing symbiotic relationships between plant growth-promoting microbes, including rhizobacteria and mycorrhizal fungi, (2) conferring biotic stress resistance by producing antibiotic compounds, and (3) secreting microbe-to-plant signal compounds, such as phytohormones or their analogues, that regulate aspects of plant physiology, including stress resistance. As plants have evolved, they recruited microbes to assist in the adaptation to available growing environments. Microbes serve themselves by promoting plant growth, which in turn provides microbes with nutrition (root exudates, a source of reduced carbon) and a desirable habitat (the rhizosphere or within plant tissues). The outcome of this coevolution is the diverse and metabolically rich microbial community that now exists in the rhizosphere of terrestrial plants. The holobiont, the unit made up of the phytomicrobiome and the plant host, results from this wide range of coevolved relationships. We are just beginning to appreciate the many ways in which this complex and subtle coevolution acts in agricultural systems.

Valerian (Valeriana officinalis L.) is a medicinal plant, but its cultivation is restricted by weed competition. Therefore, three rates (0.75X, 1X, and 1.25X, where X is equal to the recommended dose of haloxyfop-R (methyl ester), sethoxydim, oxadiargyl, bentazon, oxadiazon, and oxyfluorfen) were applied at the 3-4 leaf stages to valerian plants. This application was done to select the herbicide type and rate for post-controlling broadleaf and grasses weeds in this species. Herbicide injury, Soil-Plant Analyses Development (SPAD) reading, number of leaves per plant, stem diameter, and fresh and dry weights were determined 10, 20, and 30 days after herbicide application. Oxyfluorfen application caused the most herbicide injury followed by bentazon. Injury increased as the rate and the days after application increased. Oxadiazon only caused significant damage 30 days after application under all three rates. Other treatments showed no marked injuries under any rate or date after application, as compared with the control. Effects on other measured traits depended on the trait, herbicide, and herbicide rate. The highest SPAD, leaf number, shoot diameter, fresh weight and dry weight, was recorded under application of 30 mg a.i. ∙ kg-1soil oxadiargyl and 90 mg a.i. ∙ kg-1soil oxadiazon, 81 mg a.i. ∙ kg-1soil haloxyfop-R, 37.5 mg a.i. ∙ kg-1soil oxadiargyl, 22.5 mg a.i. ∙ kg-1soil oxadiargyl, 81 mg a.i. ∙ kg-1soil haloxyfop-R, and 81 mg a.i. ∙ kg-1soil haloxyfop-R, respectively. To sum up, the results showed that sethoxydim, oxadiargyl, and haloxyfop-R produced no significant symptoms of phytotoxicity or reduction of measured traits. This means that oxadiargyl, haloxyfop-R, and sethoxydim may be used safely for weed control of valerian at the rates used in this experiment under similar conditions.

Soil salinity is a major constraint for soybean production worldwide, and the exploitation of plant growth-promoting bacteria (PGPB) and their bioactive metabolite(s) can improve plant salinity tolerance. With this objective, two experiments were performed, aiming to test 4 culture media (YEM(A), TYE(A), TS(A), and LB(A)) for growing a novel Devosia sp. (strain SL43), and then evaluating cell-free supernatants (CFS) from the Devosia sp. on germination of soybean (Glycine max L.) seeds under salinity stress. Soybean seeds were subjected to three salinity levels (0, 100, and 125 mM NaCl) and 6 levels of Devosia sp. CFS dilution (0, 1:1, 1:100, 1:250, 1:500, 1:1000). The results indicated that 125 mM NaCl concentration caused the greatest reduction in the total number of germinated seeds (15%), germination rate (43.6%), root length (55.2%), root weight (39.3%), and seed vigor (68%), and it also increased mean germination time by 71.9%. However, Devosia-CFS improved soybean germination, and the greatest effect was obtained at 1:1 dilution. Under the highest salinity level, application of CFS at 1:1 dilution increased final germination (17.6%), germination rate (18.6%), root length (162.2%), root weight (239.4%), seed vigor index (318.7%), and also shortening mean germination time by 19.2%. The results indicated that seed vigor index was positively correlated with other traits except for mean germination time. Our study suggested that the highest productivity of Devoisa sp. was obtained from the YEM medium. Results also suggested that CFS produced by the novel Devosia sp. (SL43 strain) can successfully alleviate salt stress effects on soybean seed germination and manipulating the chemical composition of the growth medium can influence the effectiveness of these bioactive metabolites.