Land Management Legacy Affects Abundance and Function of the acdS Gene in Wheat Root Associated Pseudomonads

Abstract

Land management practices can vastly influence belowground plant traits due to chemical, physical, and biological alteration of soil properties. Beneficial Pseudomonas spp. are agriculturally relevant bacteria with a plethora of plant growth promoting (PGP) qualities, including the potential to alter plant physiology by modulating plant produced ethylene via the action of the bacterial enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase (acdS). This study evaluated the impact of land management legacy on the selection and function of wheat root associated culturable pseudomonad isolates. Three distinct previous land uses prior to wheat culture (grassland, arable, and bare fallow) were tested and culturable pseudomonad abundance, phylogeny (gyrB and acdS genes), function (ACC deaminase activity), and the co-selection of acdS with other PGP genes examined. The pseudomonad community could to some extent be discriminated based on previous land use. The isolates from rhizosphere and root compartments of wheat had a higher acdS gene frequency than the bulk soil, particularly in plants grown in soil from the bare fallow treatment which is known to have degraded soil properties such as low nutrient availability. Additionally, other genes of interest to agriculture encoding anti-fungal metabolites, siderophores, and genes involved in nitrogen metabolism were highly positively associated with the presence of the acdS gene in the long-term arable treatment in the genomes of these isolates. In contrast, genes involved in antibiotic resistance and type VI secretion systems along with nitrogen cycling genes were highly positively correlated with the acdS gene in bare fallow isolated pseudomonad. This highlights that the three land managements prior to wheat culture present different selection pressures that can shape culturable pseudomonad community structure and function either directly or indirectly via the influence of wheat roots.

Keywords: ACC deaminase; Pseudomonas; land use intensity; rhizosphere; root; wheat.

FIGURE 1

The abundance of Pseudomonas spp. isolated from bulk soil, the rhizosphere, and roots of wheat grown in soils from three different land managements. Log transformed data for the mean CFU g^–1 ± SD of Pseudomonas spp. isolated from bulk soil, the rhizosphere, and the roots of wheat grown in soils from arable, grassland, and bare fallow managed soils. Symbols sharing the same letter are not significantly (P < 0.05) different according to Tukey’s HSD post hoc test.

FIGURE 2

Maximum likelihood (ML) tree based on gyrB nucleotide sequences from genome sequenced Pseudomonas strains associated with wheat grown in soils from three different land managements. The 54 isolates from bulk soil, rhizosphere soil, and roots of wheat grown in three distinct land management regimes (bare fallow, arable, and grassland) were phylogenetically analyzed utilizing a ML tree with a transitional model. Percentage bootstrap are indicated at branching nodes. Branch labels are colored to indicate the soil management where the bacteria was isolated and boxes beside labels indicate the soil compartment. Circles indicate the presence or absence of acdS gene in the genome of the isolate.

FIGURE 3

The distribution of the acdS gene abundance across three different land managements. A total of 27 isolates possessed the acdS gene, the bar graph showing its abundance across the different niche compartments of bulk soil, rhizosphere soil, and wheat roots.

FIGURE 4

Phylogeny of the acdS gene in pseudomonads from three different land managements. acdS sequences from bulk soil, rhizosphere, and roots associated with wheat grown in three distinct land management regimes (bare fallow, arable, and grassland) were phylogenetically analyzed utilizing a ML tree with a transitional model and 1,000 bootstraps in the software PhyML. Percentage bootstrap are indicated at branching nodes. Branch labels are colored to indicate the soil management where the bacteria was isolated and boxes beside labels indicate the soil compartment.

FIGURE 5

In silico analysis of the acdS translated amino acid sequences. The amino acids Lys51, Ser78, Tyr294, Glu295, and Leu322 have all been implicated as essential for the functioning of the acdS gene in the reference isolate Pseudomonas sp. UW4. The alignments shown here with amino acid sequences translated from the acdS gene were each found to have all 5 amino acids in the same position as the reference isolate Pseudomonas sp. UW4.

FIGURE 6

1-Aminocyclopropane-1-carboxylate consumption by isolates with the acdS gene grown in media with ACC as the sole nitrogen source. The mean ACC consumption for isolates from arable, bare fallow, and grassland treatments, grown in Dworkin and Foster (DF) + ACC medium with ACC concentration quantified by a ninhydrin colorimeter test at 24 and 48 h post inoculation.

FIGURE 7

Gene presence/absence correlation coefficient analysis. Spearman’s rank correlation coefficients between the presence or absence of a selection of PGPR traits correlated against the presence of the acdS gene in bacterial isolates from three distinct land managements. The scale range is from dark blue (highly negatively correlated) to bright red (highly positively correlated), light colors represent low correlations.