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Full Paper • J. Braz. Chem. Soc. 37 (spe1) • 2026 • https://doi.org/10.21577/0103-5053.20260040 linkcopy

Metabolomic Insights on Plant Growth-Promoting Yeast as Bioinput: Biochemical Interactions with Tomato Seedlings

Authorship SCIMAGO INSTITUTIONS RANKINGS

Abstract

Plant growth-promoting yeasts (PGPYs)-based bioinputs offer a sustainable approach in agriculture, increasing crop productivity and reducing environmental impacts. However, their chemical interactions with plants remain poorly understood. In this paper, metabolites and metabolic pathways were deeply investigated in tomato seedling leaves inoculated with active (L01AT) and inactive (L01IN) Sporidiobolus yeast. Yeast was applied near the roots of the tomato seedlings, and agronomic and metabolomic studies were performed after 40 days. A total of 73 metabolites, including primary and secondary, were annotated using mass spectrometry-based metabolomics. Inoculation of the yeast L01AT promotes more intense changes in the biosynthetic pathways of secondary metabolism compounds, such as phenylpropanoid biosynthesis, such as phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, and anthocyanin biosynthesiss. On the other hand, inoculation of the yeast L01IN promotes changes in the primary metabolic pathways, such as lysine biosynthesis and porphyrin metabolism, which are compounds derived from yeast cell degradation after heating. This integrated agronomic, biological, and chemical analysis provides a comprehensive understanding of the metabolic reprogramming induced by Sporidiobolus inoculation in tomato seedlings. These findings contribute to the design of safer and more efficient bioinput strategies and support the discovery of bioactive compounds for advanced formulation development.

Keywords:
mass spectrometry; metabolomics; metabolites; metabolic pathways; sustainable agriculture

Agronomic parameter	Code	Score
Stem diameter	SD	1
Root length	RL	2
Plant height	H	3
Root fresh mass	RFM	4
Shoot fresh mas	AFM	5
Total fresh mass	TFM	6
Root dry mass	RDM	7
Shoot dry mass	ADM	8
Total dry mass	TDM	9
Dickson quality index	QDI	10

	Treatment	Agronomic parameter										Total
	Treatment	H	RL	SD	AFM	RFM	TFM	ADM	RDM	TDM	QDI	Total
01	L01IN											52
02	L01AT											13
03	CF											0

Sample	Metabolic pathway	Classification
L01AT	phenylpropanoid biosynthesis	secondary metabolism
	flavone and flavonol biosynthesis	secondary metabolism
	anthocyanin biosynthesis	secondary metabolism
	cutin, suberin and wax biosynthesis	primary metabolism
	phenylalanine, tyrosine and tryptophan biosynthesis	primary metabolism
L01IN	monobactam biosynthesis	secondary metabolism
	lysine biosynthesis	primary metabolism
	porphyrin metabolism	primary metabolism
	flavone and flavonol biosynthesis	secondary metabolism
	biosynthesis of various plant secondary metabolites	secondary metabolism

Compound name	Molecular formula	Adduct	m/z	Mass difference	Cosine	Retention time / min	Classification
Quinate	C₇H₁₂O₆	[M - H]^-	191.056	0.0003	0.938	0.652	primary/organic acids
Citric acid	C₆H₁₁NO₇	[M + H]⁺	210.061	0.0012	0.760	0.864	primary/organic acids
Pipecolic acid	C₆H₁₁NO₂	[M + H]⁺	130.05	0.036	0.933	0.609	primary/amino acid
Arginine	C₆H₁₄N₄O₂	[M + H]⁺	175.119	0.000	0.754	0.533	primary/amino acid
Phenylalanine	C₉H₁₁NO₂	[M + H]⁺	166.086	0.000	0.906	2.002	primary/amino acid
Glutamine	C₅H₁₀N₂O₃	[2M + H]⁺	293.146	0.001	0.732	0.595	primary/amino acid
Lysine	C₆H₁₄N₂O₂	[M + H]⁺	147.076	0.037	0.964	0.595	primary/amino acid
Tyrosine	C₉H₁₂NO₃	[M + H]⁺	182.081	0.000	0.983	0.972	primary/amino acid
Trehalose	C₁₇H₃₀O₁₅	[M - H₂O + H]⁺	457.156	0.001	0.774	6.264	primary/carbohydrates
Sucrose	C₁₂H₂₂O₁₁	[M + NH₄]⁺	360.149	0.001	0.914	0.618	primary/carbohydrates
5,6-Epoxy-8Z,11Z,14Z-eicosatrienoic acid	C₂₅H₄₇NO	[M - H₂O + H]⁺	304.301	0.000	0.777	10.159	primary/lipids
Heptadecasfing-4-enine	C₂₁H₄₂N₂O₃	[M + H]⁺	371.328	0.000	0.865	9.543	primary/lipids
Lyso-PC(16:0)	C₂₆H₄₈NO₇P	[M + H]⁺	518.325	0.001	0.750	9.737	primary/lipids
1-Stearoyl-2-hydroxy-sn-glycero-3‑phosphoethanolamine	C₂₃H₄₄NO₇P	[M + H]⁺	478.295	0.002	0.781	10.416	primary/lipids
1-Palmitoyl-2-hydroxy-sn-glycero-3‑phosphoethanolamine	C₃₉H₄₀O₄	[M + H]⁺	573.305	0.002	0.808	10.949	primary/nucleotide
Adenine	C₅H₅N₅	[M + H]⁺	136.062	0.000	0.817	0.655	secondary/carboxylic acid
Coumaroylquinic acid	C₁₆H₁₈O₈	[M + H]⁺	339.107	0.000	0.838	4.778	secondary/alkaloids
Tyramine	C₈H₁₁NO	[M + H-NH₃]⁺	121.064	0.001	0.738	1.126	secondary/alkaloids
Solasodine	C₂₇H₄₅NO₂	[M + H]⁺	416.354	0.002	0.833	6.264	secondary/alkaloids
Tomatidine	C₃₃H₅₅NO₇	[M + H]⁺	578.408	0.003	0.916	6.254	secondary/phenolic compounds
1-[4-Hydroxy-3-(3-methylbut-2-enyl)phenyl]ethanone	C₁₃H₁₆O₂	[M + H]⁺	205.086	0.036	0.845	11.811	secondary/phenolic compounds
2-(3,4-Dihydroxyphenyl)-5-hydroxy-7‑[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6‑[[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxymethyl]oxan-2-yl]oxychromen-4-one	C₂₇H₃₀O₁₅	[M + H]⁺	595.166	0.001	0.976	5.415	secondary/phenolic compounds
2-(3,4-Dihydroxyphenyl)-5,7-dihydroxy-3-(((2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-((((3R,4R,5R,6S)-3,4,5 -trihydroxy-6‑methyltetrahydro-2H-pyran-2-yl)oxy)methyl)tetrahydro-2H-pyran-2-yl)oxy)-4H-chromen-4-one	C₂₇H₃₀O₁₆	[M + Na]⁺	633.143	0.003	0.851	5.118	secondary/phenolic compounds
2-(Hydroxymethyl)-6-[4-[(2S,3S)-3‑(hydroxymethyl)-5-[(E)-3-hydroxyprop-1‑enyl]-7-methoxy-2,3-dihydro-1-benzofuran-2-yl]-2-methoxyphenoxy]oxane-3,4,5-triol	C₂₆H₃₂O₁₁	[M + NH₄]⁺	538.229	0.001	0.746	5.224	secondary/compounds phenolics
3-[(2S,3R,4S,5S,6R)-6-[[(2R,3R,4R,5R,6S)-3‑[(2S,3R,4R)-3,4-Dihydroxy-4‑(hydroxymethyl)oxolan-2-yl]oxy-4,5‑dihydroxy-6-methyloxan-2-yl]oxymethyl]-3,4,5-trihydroxyoxan-2-yl]oxy-2‑(3,4‑dihydroxyphenyl)-5,7‑dihydroxychromen-4-one	C₃₂H₃₈O₂₀	[M + H]⁺	743.206	0.003	0.874	4.854	secondary/phenolic compounds
3-[4,5-Dihydroxy-6-(hydroxymethyl)-3‑[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6‑methyloxan-2-yl]oxyoxan-2-yl]oxy-5‑hydroxy-2-(4-hydroxyphenyl)-7-[3,4,5‑trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxychromen-4-one	C₃₃H₄₀O₂₀	[M + H]⁺	757.223	0.005	0.822	4.382	secondary/phenolic compounds
(E)-3-[4-[(2S,3R,4S,5S,6R)-3,4,5-Trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyphenyl]prop-2-enoic acid	C₁₅H₁₈O₈	[M + NH₄]⁺	344.134	0.000	0.846	4.219	secondary/phenolic compounds
Cryptochlorogenic acid	C₁₆H₁₈O₉	[M + H]⁺	355.103	0.000	0.954	4.178	secondary/phenolic compounds
Coumaric acid	C₉H₈O₃	[M + H]⁺	165.054	0.001	0.843	4.222	secondary/phenolic compounds
Furostane base + O-Hex, O-Hex-Hex-Hex	C₄₆H₈₁N₇O₂₀	[M - H₂O + H]⁺	1034.56	0.008	0.866	6.236	secondary/phenolic compounds
Kaempferol-3-O-rutinoside	C₂₇H₃₀O₁₅	[M - H]^-	593.152	0.0477	0.932	5.436	secondary/phenolic compounds
Quercetin-4’-O-glucoside	C₂₁H₂₀O₁₂	[M + H]⁺	465.103	0.000	0.846	5.118	secondary/phenolic compounds
Roseoside	C₁₉H₃₀O₈	[M + H]⁺	387.201	0.002	0.733	4.742	secondary/phenolic compounds
Routine	C₂₇H₃₀O₁₆	[M - H]^-	609.147	0.0013	0.995	5.137	secondary/phenolic compounds
4-[(E)-3-[(2R,3R,4S,5S,6R)-3-[(2S,3R,4R)-3,4‑Dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy-4,5-dihydroxy-6-(hydroxymethyl)oxan-2‑yl]oxybut-1-enyl]-3,5,5-trimethylcyclohex-2-en-1-one	C₂₂H₃₂O₁₀	[M + H]⁺	457.207	0.002	0.721	6.092	secondary/terpenoids
Canrenone	C₁₃H₃₀NO₅S	[M - H]^-	311.168	0.0105	0.899	11.341	secondary/terpenoids

Compound name	Molecular formula	Adduct	m/z	Mass difference	Cosine	Retention time / min	Classification
Citric acid	C₆H₈O₇	[M - H]^-	191.02	0.0151	0.958	0.888	primary/organic acids
Isocitric acid	C₆H₈O₇	[M + H]⁺	224.129	0.001	0.743	3.54	primary/organic acids
Quinic acid	C₇H₁₂O₆	[M - H]^-	191.056	0	0.963	0.647	primary/organic acids
Pipecolic acid	C₆H₁₁NO₂	[M + H]⁺	130.05	0.036	0.918	0.6	primary/amino acids
Arginine	C₆H₁₄N₄O₂	[M + H]⁺	175.118	0.001	0.752	0.55	primary/amino acids
Glutamine	C₅H₁₀N₂O₃	[2M + H]⁺	293.146	0.001	0.836	0.577	primary/amino acids
Lysine	C₆H₁₄N₂O₂	[M + H]⁺	147.076	0.037	0.941	0.605	primary/amino acids
Tyrosine	C₉H₁₁NO₃	[M + H]⁺	182.081	0.004	0.805	0.989	primary/amino acids
Myristamidopropyl betaine	C₁₉H₃₈N₂O₃	[M + H]⁺	343.296	0	0.903	8.461	primary/amino acids
Alpha-galactose 1-phosphate	C₆H₁₃O₉P	[M - H]^-	259.022	0	0.954	0.589	primary/carbohydrates
Trehalose	C₁₇H₃₀O₁₅	[M - H₂O + H]⁺	457.155	0.002	0.788	6.262	primary/carbohydrates
Rutinose	C₁₁H₂₀O₁₀	[M - H₂O + H]⁺	295.102	0.001	0.855	6.262	primary/carbohydrates
Sucrose	C₁₂H₂₂O₁₁	[M + NH₄]⁺	360.15	0	0.926	0.618	primary/carbohydrates
Heptadecasfing-4-enina	C₂₁H₄₂N₂O₃	[M + H]⁺	371.327	0.001	0.865	9.552	primary/lipids
Adenine	C₅H₅N₅	[M + H]⁺	136.062	0	0.751	0.665	primary/nucleotides
Adenosine	C₁₀H₁₃N₅O₄	[M + H]⁺	268.104	0	0.94	1.013	primary/nucleotides
N-Methylnicotinate	C₇H₇NO₂	[M + H]⁺	138.055	0	0.93	0.618	secondary/alkaloids
Solasodine	C₂₇H₄₅NO₂	[M + H]⁺	416.353	0	0.851	6.262	secondary/alkaloids
Tomatidine	C₃₃H₅₅NO₇	[M + H]⁺	578.407	0.002	0.913	6.262	secondary/alkaloids
Acanthoside B	C₂₈H₃₆O₁₃	[M + NH₄]⁺	598.249	0	0.829	5.648	secondary/phenolic compounds
(E)-3-[4-[(2S,3R,4S,5S,6R)-3,4,5-Trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyphenyl]prop-2-enoic acid	C₁₅H₁₈O₈	[M + NH₄]⁺	344.134	0	0.811	4.225	secondary/phenolic compounds
Curcumin	C₁₆H₁₈O₉	[M + H]⁺	355.101	0.001	0.921	4.178	secondary/phenolic compounds
Delphinidin 3-galactoside	C₂₁H₂₁ClO₁₂	[M + Cl]^-	465.102	0	0.857	5.135	secondary/phenolic compounds
2-(3,4-Dihydroxyphenyl)-5-hydroxy- 7-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy- 6-[[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxymethyl]oxan-2-yl]oxychromene-4-one	C₂₇H₃₀O₁₅	[M + H]⁺	595.166	0.001	0.946	5.439	secondary/phenolic compounds
2-(Hydroxymethyl)-6-[4-[(2S,3S)- 3-(hydroxymethyl)-5-[(E)-3-hydroxy prop- 1-enyl]-7-methoxy-2,3-dihydro-1-benzofuran-2-yl]-2-methoxyphenoxy]oxane-3,4,5-triol	C₂₆H₃₂O₁₁	[M + NH₄]⁺	538.228	0	0.784	5.227	secondary/phenolic compounds
3-[(2S,3R,4S,5S,6R)-6-[[(2R,3R,4R,5R,6S)- 3-[(2S,3R,4R)-3,4-Dihydroxy- 4-(hydroxymethyl)oxolan-2-yl]oxy- 4,5-dihydroxy-6-methyloxan-2-yl]oxymethyl]-3,4,5-trihydroxyoxan-2-yl]oxy- 2-(3,4-dihydroxyphenyl)- 5,7-dihydroxychromen-4-one	C₃₂H₃₈O₂₀	[M + H]⁺	743.201	0.002	0.844	4.874	secondary/phenolic compounds
3-O-Feruloylquinic acid	C₁₇H₂₀O₉	[M - H]^-	367.103	0.0002	0.843	4.887	secondary/phenolic compounds
Coumaroylquinic acid	C₁₆H₁₈O₈	[M - H]^-	337.093	0.0007	0.8855	4.665	secondary/phenolic compounds
Kaempferol 3-O-rutinoside	C₃₂H₃₈O₁₉	[M + H]⁺	727.209	0.001	0.869	5.089	secondary/phenolic compounds
Kaempferol-3-glucoside-3”-rhamnoside	C₂₇H₃₀O₁₅	[M + H]⁺	593.151	0	0.965	5.433	secondary/phenolic compounds
Routine	C₂₇H₃₀O₁₆	[M - H]^-	609.147	0.001	0.982	5.141	secondary/phenolic compounds
3-[4,5-Dihydroxy-6-(hydroxymethyl)- 3-[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy- 6-methyloxan-2-yl]oxyoxan-2-yl]oxy- 5-hydroxy-2-(4-hydroxyphenyl)- 7-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan- 2-yl]oxychromen-4-one	C₄₅H₄₄O₁₉	[M + H]⁺	889.252	0.009	0.784	4.15	secondary/flavonoids
(R)-Linalyl beta-vicianoside	C₂₁H₃₆O₁₀	[M + NH₄]⁺	466.265	0	0.798	6.537	secondary/terpenoids
4-[(E)-3-[(2R,3R,4S,5S,6R)-3-[(2S,3R,4R)- 3,4-Dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy-4,5-dihydroxy-6-(hydroxymethyl)oxan- 2-yl]oxybut-1-enyl]-3,5,5-trimethylcyclohex-2-en-1-one	C₂₂H₃₂O₁₀	[M + H]⁺	457.206	0.003	0.824	6.027	secondary/terpenoids
Canrenone	C₁₃H₃₂N₃O₄S	[M - H]^-	325.185	0.021	0.893	12.377	secondary/terpenoids
Furostan	C₄₆H₈₁N₇O₂₀	[M - H₂O + H]⁺	1034.56	0.007	0.925	6.281	secondary/terpenoids
Harpagide	C₁₅H₂₄O₁₀	[M + H]⁺	365.105	0.035	0.831	0.627	secondary/terpenoids

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