In-Situ Metabolomic Analysis of Setaria viridis Roots Colonized by Beneficial Endophytic Bacteria

Abstract

Over the past decades, crop yields have risen in parallel with increasing use of fossil fuel–derived nitrogen (N) fertilizers but with concomitant negative impacts on climate and water resources. There is a need for more sustainable agricultural practices, and biological nitrogen fixation (BNF) could be part of the solution. A variety of nitrogen-fixing, epiphytic, and endophytic plant growth–promoting bacteria (PGPB) are known to stimulate plant growth. However, compared with the rhizobium-legume symbiosis, little mechanistic information is available as to how PGPB affect plant metabolism. Therefore, we investigated the metabolic changes in roots of the model grass species Setaria viridis upon endophytic colonization by Herbaspirillum seropedicae SmR1 (fix+) or a fix− mutant strain (SmR54) compared with uninoculated roots. Endophytic colonization of the root is highly localized and, hence, analysis of whole-root segments dilutes the metabolic signature of those few cells impacted by the bacteria. Therefore, we utilized in-situ laser ablation electrospray ionization mass spectrometry to sample only those root segments at or adjacent to the sites of bacterial colonization. Metabolites involved in purine, zeatin, and riboflavin pathways were significantly more abundant in inoculated plants, while metabolites indicative of nitrogen, starch, and sucrose metabolism were reduced in roots inoculated with the fix− strain or uninoculated, presumably due to N limitation. Interestingly, compounds, involved in indole-alkaloid biosynthesis were more abundant in the roots colonized by the fix− strain, perhaps reflecting a plant defense response.

The plant endosphere world – bacterial life within plants

“…These -omics methods can be complemented by other approaches, such as confocal microscopy, which, after inoculation of a strain into an axenic plant, makes it possible to verify that the strain is indeed an endophyte and to identify the tissues it colonizes (Bünger et al, 2020). Agtuca et al (2020) combined confocal and fluorescence imaging with in situ metabalomics to discover the metabolites that are over-expressed in plant tissues colonized by an endophytic bacterium. The future challenge in plant endophyte research is, however, not only to master and combine advanced tools, but also to link research questions to conceptual frameworks (Saikkonen et al, 2020).…”

Response of Nitrogen Metabolism in Masson Pine Needles to Elevated CO2

“…Noteworthily, the previous studies have shown that the nitrogen fixation ability and the changes of nitrogen in plants are also affected by soil fertility [51,52], soil microorganisms [53,54] or metal elements [55]. We studied the change of elevated CO 2 content as the main factor but did not verify or discuss the influence of other factors on nitrogen metabolism of Masson pine under the same condition.…”

Diverse Bacterial Genes Modulate Plant Root Association by Beneficial Bacteria

“…H. seropedicae SmR1 is a well-studied endophytic bacterium that colonizes several plants, including maize, wheat, and Setaria. Recently, in situ metabolomic profiling of S. viridis roots colonized by SmR1 demonstrated that inoculation induced a wide variety of plant metabolic changes, including those affecting nitrogen and phytohormone levels (15). Thus, similar to many other, better-studied plant-microbe associations, PGPB inoculation appears to profoundly affect the metabolism of its host.…”