Metagenomic Analysis of the Bacterial Community Associated with the Taproot of Sugar Beet

Abstract

We analyzed a metagenome of the bacterial community associated with the taproot of sugar beet (Beta vulgaris L.) in order to investigate the genes involved in plant growth-promoting traits (PGPTs), namely 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, indole acetic acid (IAA), N2 fixation, phosphate solubilization, pyrroloquinoline quinone, siderophores, and plant disease suppression as well as methanol, sucrose, and betaine utilization. The most frequently detected gene among the PGPT categories encoded β-1,3-glucanase (18 per 105 reads), which plays a role in the suppression of plant diseases. Genes involved in phosphate solubilization (e.g., for quinoprotein glucose dehydrogenase), methanol utilization (e.g., for methanol dehydrogenase), siderophore production (e.g. isochorismate pyruvate lyase), and ACC deaminase were also abundant. These results suggested that such PGPTs are crucially involved in supporting the growth of sugar beet. In contrast, genes for IAA production (iaaM and ipdC) were less abundant (~1 per 105 reads). N2 fixation genes (nifHDK) were not detected; bacterial N2 -fixing activity was not observed in the 15N2 -feeding experiment. An analysis of nitrogen metabolism suggested that the sugar beet microbiome mainly utilized ammonium and nitroalkane as nitrogen sources. Thus, N2 fixation and IAA production did not appear to contribute to sugar beet growth. Taxonomic assignment of this metagenome revealed the high abundance of Mesorhizobium, Bradyrhizobium, and Streptomyces, suggesting that these genera have ecologically important roles in the taproot of sugar beet. Bradyrhizobium-assigned reads in particular were found in almost all categories of dominant PGPTs with high abundance. The present study revealed the characteristic functional genes in the taproot-associated microbiome of sugar beet, and suggest the opportunity to select sugar beet growth-promoting bacteria.

Impact of plants on the diversity and activity of methylotrophs in soil

“…To investigate differences in the abundance and diversity of methanol dehydrogenase-encoding genes in the three methanol-enriched soil habitats, the assembled and unassembled reads of the metagenomes were screened with representative sequences of each clade of methanol dehydrogenase-encoding gene (xoxF1, xoxF2, xoxF3, xoxF4, xoxF5, mxaF and mdh2). The abundance of methanol dehydrogenase genes differed between the three metagenomes (Additional Files 11,12,13,14,15,16). mxaF and xoxF4 were present at higher abundance in the two plant habitats relative to the unplanted soil, whereas xoxF5 and xoxF3 were more abundant in the pea rhizosphere relative to the unplanted soil and wheat rhizosphere.…”

“…Previous studies have indicated that methylotrophic bacteria are enriched in the rhizosphere of certain plant species, for example, Methylobacteraceae and Hyphomicrobiaceae in the rhizosphere of Arabidopsis thaliana [12], Methylophilaceae and Comamonadaceae in the pea rhizosphere and Methylophilaceae and Methylocaldum in the wheat rhizosphere [13]. Methanol dehydrogenase genes have been detected in the rhizosphere of rice, grasses, soybeans, cereals and pea plants [14][15][16], methanol dehydrogenase enzymes have been detected in the rhizosphere soils of oat, wheat and A. thaliana [17], and soils in association with A. thaliana had higher rates of methanol dissimilation than non-plantassociated soils [18]. However, the reasons for changes in the abundance of methylotrophs in the soil in response to plant growth are hard to identify, since many of these methylotrophs can also use multi-carbon compounds, which could be supplied either directly from the plant or from the exudate-induced accelerated breakdown of recalcitrant soil organic matter (SOM) [19].…”

Bacterial endophytes in agricultural crops and their role in stress tolerance: a review

“…However, application of culture independent methods allowed studies of growing numbers of plant material samples and revealed rarely reported endophyte species of δ-and ε-proteobacteria in rice roots (Sun et al, 2008). Tsurumaru et al (2015) analyzed a metagenome of the bacterial community associated with the taproot of sugar beet (Beta vulgari L.) The study found that Alphaproteobacteria are dominant, followed by the Actinobacteria and the Betaproteobacteria. Another metagenomic study of the sorghum root and stem microbiome revealed that the two tissues harboured significantly different composition of bacterial communities, but both were dominated by agriculturally important genera such as Microbacterium, Agrobacterium, Sphingobacterium, Herbaspirillum, Erwinia, Pseudomonas and Stenotrophomonas (Maropola et al, 2015).…”

Stable isotope informed genome-resolved metagenomics uncovers potential trophic interactions in rhizosphere soil

“…We targeted interaction signatures such as genes for the production of plant hormones and modulation of hormone concentrations, secretion systems, and secondary metabolites. Assembled genomes enabled the prediction of whether an organism is a plant growth-promoting bacteria (PGPB) or a pathogen (36,37).…”