Identification of Root-Associated Bacteria That Influence Plant Physiology, Increase Seed Germination, or Promote Growth of the Christmas Tree Species Abies nordmanniana

Abies nordmanniana is used for Christmas tree production but poor seed germination and slow growth represent challenges for the growers. We addressed the plant growth promoting potential of root-associated bacteria isolated from A. nordmanniana. Laboratory screenings of a bacterial strain collection yielded several Bacillus and Paenibacillus strains that improved seed germination and produced indole-3-acetic acid. The impact of three of these strains on seed germination, plant growth and growth-related physiological parameters was then determined in greenhouse and field trials after seed inoculation, and their persistence was assessed by 16S rRNA gene-targeted bacterial community analysis. Two strains showed distinct and significant effects. Bacillus sp. s50 enhanced seed germination in the greenhouse but did not promote shoot or root growth. In accordance, this strain did not increase the level of soluble hexoses needed for plant growth but increased the level of storage carbohydrates. Moreover, strain s50 increased glutathione reductase and glutathione-S-transferase activities in the plant, which may indicate induction of systemic resistance during the early phase of plant development, as the strain showed poor persistence in the root samples (rhizosphere soil plus root tissue). Paenibacillus sp. s37 increased plant root growth, especially by inducing secondary root formation, under in greenhouse conditions, where it showed high persistence in the root samples. Under these conditions, it further it increased the level of soluble carbohydrates in shoots, and the levels of starch and non-structural carbohydrates in roots, stem and shoots. Moreover, it increased the chlorophyll level in the field trial. These findings indicate that this strain improves plant growth and vigor through effects on photosynthesis and plant carbohydrate reservoirs. The current results show that the two strains s37 and s50 could be considered for growth promotion programs of A. nordmanniana in greenhouse nurseries, and even under field conditions.

Effects of Intra- and Interspecific Plant Density on Rhizosphere Bacterial Communities

There have been very few studies on the effects of plant competition on the rhizosphere bacterial community. To investigate the impacts of intra- and interspecific plant competition, we analyzed the responses of rhizosphere bacterial communities to plant density as determined by 16S rRNA gene targeted sequencing. We included five weedy plant species growing in field soil in monocultures and mixed cultures at three densities in a greenhouse experiment. The rhizosphere bacterial community of each species changed more with density in a mixture of all five plant species than in monocultures, so intra- and interspecific plant competition had different effects on the bacterial community. For the dominant plant competitor, Centaurea cyanus, neither intra- nor interspecific competition had major effects on the composition of its rhizosphere bacterial communities. In contrast, the bacterial communities of the weakest competitor, Trifolium repens, were affected differently by intra- and interspecific competition. During increasing intraspecific competition T. repens maintained a highly specialized bacterial community dominated by Rhizobium; while during interspecific competition, the relative abundance of Rhizobium declined while other nitrogen fixing and potentially plant growth promoting taxa became more abundant. Contrary to previous observations made for soil microbial communities, the bacterial rhizosphere community of the weakest competitor did not become more similar to that of the dominant species. Thus, the process of competition, as well as the plant species themselves, determined the rhizosphere bacterial community. Our results emphasize the role of plant-plant interactions for rhizosphere bacterial communities. These effects may feedback to affect plant-plant interactions, and this is an important hypothesis for future research.

Under the Christmas Tree: Belowground Bacterial Associations With Abies nordmanniana Across Production Systems and Plant Development

Abies nordmanniana is an economically important tree crop widely used for Christmas tree production. After initial growth in nurseries, seedlings are transplanted to the field. Rhizosphere bacterial communities generally impact the growth and health of the host plant. However, the dynamics of these communities during A. nordmanniana growth in nurseries, and during transplanting, has not previously been addressed. By a 16S rRNA gene amplicon sequencing approach, we characterized the composition and dynamics of bacterial communities in the rhizosphere during early plant growth in field and greenhouse nurseries and for plants transplanted from the greenhouse to the field. Moreover, the N-cycling potential of rhizosphere bacteria across plant age was addressed in both nurseries. Overall, a rhizosphere core microbiome of A. nordmanniana, comprising 19.9% of the taxa at genus level, was maintained across plant age, nursery production systems, and even during the transplantation of plants from the greenhouse to the field. The core microbiome included the bacterial genera Bradyrhizobium, Burkholderia, Flavobacterium, Pseudomonas, Rhizobium, Rhodanobacter, and Sphingomonas, which harbor several N-fixing and plant growth–promoting taxa. Nevertheless, both plant age and production system caused significant changes in the rhizosphere bacterial communities. Concerning community composition, the relative abundance of Rhizobiales (genera Rhizobium, Bradyrhizobium, and Devosia) was higher in the rhizosphere of field-grown A. nordmanniana, whereas the relative abundance of Enterobacteriales and Pseudomonadales (genus Pseudomonas) was higher in the greenhouse. Analysis of community dynamics across plant age showed that in the field nursery, the most abundant bacterial orders showed more dynamic changes in their relative abundance in the rhizosphere than in the bulk soil. In the greenhouse, age-dependent dynamics even occurred but affected different taxa than for the field-grown plants. The N-cycling potential of rhizosphere bacterial communities showed an increase of the relative abundance of genes involved in nitrogen fixation and denitrification by plant age. Similarly, the relative abundance of reported nitrogen-fixing or denitrifying bacteria increased by plant age. However, different community structures seemed to lead to an increased potential for nitrogen fixation and denitrification in the field versus greenhouse nurseries.

Identification of Root-Associated Bacteria That Influence Plant Physiology, Increase Seed Germination, or Promote Growth of the Christmas Tree Species Abies nordmanniana

Abies nordmanniana is used for Christmas tree production but poor seed germination and slow growth represent challenges for the growers. We addressed the plant growth promoting potential of root-associated bacteria isolated from A. nordmanniana. Laboratory screenings of a bacterial strain collection yielded several Bacillus and Paenibacillus strains that improved seed germination and produced indole-3-acetic acid. The impact of three of these strains on seed germination, plant growth and growth-related physiological parameters was then determined in greenhouse and field trials after seed inoculation, and their persistence was assessed by 16S rRNA gene-targeted bacterial community analysis. Two strains showed distinct and significant effects. Bacillus sp. s50 enhanced seed germination in the greenhouse but did not promote shoot or root growth. In accordance, this strain did not increase the level of soluble hexoses needed for plant growth but increased the level of storage carbohydrates. Moreover, strain s50 increased glutathione reductase and glutathione-S-transferase activities in the plant, which may indicate induction of systemic resistance during the early phase of plant development, as the strain showed poor persistence in the root samples (rhizosphere soil plus root tissue). Paenibacillus sp. s37 increased plant root growth, especially by inducing secondary root formation, under in greenhouse conditions, where it showed high persistence in the root samples. Under these conditions, it further it increased the level of soluble carbohydrates in shoots, and the levels of starch and non-structural carbohydrates in roots, stem and shoots. Moreover, it increased the chlorophyll level in the field trial. These findings indicate that this strain improves plant growth and vigor through effects on photosynthesis and plant carbohydrate reservoirs. The current results show that the two strains s37 and s50 could be considered for growth promotion programs of A. nordmanniana in greenhouse nurseries, and even under field conditions.

Root-Associated Microbial Communities of Abies nordmanniana: Insights Into Interactions of Microbial Communities With Antioxidative Enzymes and Plant Growth

Abies nordmanniana is a major Christmas tree species in Europe, but their uneven and prolonged growth slows down their production. By a 16S and 18S rRNA gene amplicon sequencing approach, we performed a characterization of root-associated bacterial and fungal communities for three-year-old A. nordmanniana plants collected from two nurseries in Denmark and Germany and displaying different growth patterns (small versus tall plants). Proteobacteria had the highest relative abundance at both sampling sites and plant sizes, and Ascomycota was the most abundant fungal phylum. At the order level, Acidobacteriales, Actinomycetales, Burkholderiales, Rhizobiales, and Xanthomonadales represented the bacterial core microbiome of A. nordmanniana, independently of the sampling site or plant size, while the fungal core microbiome included members of the Agaricales, Hypocreales, and Pezizales. Principal Coordinate Analysis indicated that both bacterial and fungal communities clustered according to the sampling site pointing to the significance of soil characteristics and climatic conditions for the composition of root-associated microbial communities. Major differences between communities from tall and small plants were a dominance of the potential pathogen Fusarium (Hypocreales) in the small plants from Germany, while Agaricales, that includes reported beneficial ectomycorrhizal fungi, dominated in the tall plants. An evaluation of plant root antioxidative enzyme profiles showed higher levels of the antioxidative enzymes ascorbate peroxidase, peroxidase, and superoxide dismutase in small plants compared to tall plants. We suggest that the higher antioxidative enzyme activities combined with the growth arrest phenotype indicate higher oxidative stress levels in the small plants. Additionally, the correlations between the relative abundances of specific taxa of the microbiome with the plant antioxidative enzyme profiles were established. The main result was that many more bacterial taxa correlated positively than negatively with one or more antioxidative enzyme activity. This may suggest that the ability of bacteria to increase plant antioxidative enzyme defenses is widespread.