Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont <named-content content-type="genus-species">Sinorhizobium fredii</named-content> Using Constraint-Based Modeling

ABSTRACT Rhizobia are soil bacteria able to establish symbiosis with diverse host plants. Specifically, Sinorhizobium fredii is a soil bacterium that forms nitrogen-fixing root nodules in diverse legumes, including soybean. The strain S. fredii CCBAU45436 is a dominant sublineage of S. fredii that n...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Carolina A. Contador, Siu-Kit Lo, Siu H. J. Chan, Hon-Ming Lam
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	bacteroid metabolic model nitrogen fixation rhizobia symbiosis Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/f55c39bcb6fa4a77bf055e2e910b5f2a
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:f55c39bcb6fa4a77bf055e2e910b5f2a
record_format	dspace
spelling	oai:doaj.org-article:f55c39bcb6fa4a77bf055e2e910b5f2a2021-12-02T18:39:47ZMetabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont <named-content content-type="genus-species">Sinorhizobium fredii</named-content> Using Constraint-Based Modeling10.1128/mSystems.00516-192379-5077https://doaj.org/article/f55c39bcb6fa4a77bf055e2e910b5f2a2020-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00516-19https://doaj.org/toc/2379-5077ABSTRACT Rhizobia are soil bacteria able to establish symbiosis with diverse host plants. Specifically, Sinorhizobium fredii is a soil bacterium that forms nitrogen-fixing root nodules in diverse legumes, including soybean. The strain S. fredii CCBAU45436 is a dominant sublineage of S. fredii that nodulates soybeans in alkaline-saline soils in the Huang-Huai-Hai Plain region of China. Here, we present a manually curated metabolic model of the symbiotic form of Sinorhizobium fredii CCBAU45436. A symbiosis reaction was defined to describe the specific soybean-microsymbiont association. The performance and quality of the reconstruction had a 70% score when assessed using a standardized genome-scale metabolic model test suite. The model was used to evaluate in silico single-gene knockouts to determine the genes controlling the nitrogen fixation process. One hundred forty-one of 541 genes (26%) were found to influence the symbiotic process, wherein 121 genes were predicted as essential and 20 others as having a partial effect. Transcriptomic profiles of CCBAU45436 were used to evaluate the nitrogen fixation capacity in cultivated versus in wild soybean inoculated with the microsymbiont. The model quantified the nitrogen fixation activities of the strain in these two hosts and predicted a higher nitrogen fixation capacity in cultivated soybean. Our results are consistent with published data demonstrating larger amounts of ureides and total nitrogen in cultivated soybean than in wild soybean. This work presents the first metabolic network reconstruction of S. fredii as an example of a useful tool for exploring the potential benefits of microsymbionts to sustainable agriculture and the ecosystem. IMPORTANCE Nitrogen is the most limiting macronutrient for plant growth, and rhizobia are important bacteria for agriculture because they can fix atmospheric nitrogen and make it available to legumes through the establishment of a symbiotic relationship with their host plants. In this work, we studied the nitrogen fixation process in the microsymbiont Sinorhizobium fredii at the genome level. A metabolic model was built using genome annotation and literature to reconstruct the symbiotic form of S. fredii. Genes controlling the nitrogen fixation process were identified by simulating gene knockouts. Additionally, the nitrogen-fixing capacities of S. fredii CCBAU45436 in symbiosis with cultivated and wild soybeans were evaluated. The predictions suggested an outperformance of S. fredii with cultivated soybean, consistent with published experimental evidence. The reconstruction presented here will help to understand and improve nitrogen fixation capabilities of S. fredii and will be beneficial for agriculture by reducing the reliance on fertilizer applications.Carolina A. ContadorSiu-Kit LoSiu H. J. ChanHon-Ming LamAmerican Society for Microbiologyarticlebacteroidmetabolic modelnitrogen fixationrhizobiasymbiosisMicrobiologyQR1-502ENmSystems, Vol 5, Iss 1 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	bacteroid metabolic model nitrogen fixation rhizobia symbiosis Microbiology QR1-502
spellingShingle	bacteroid metabolic model nitrogen fixation rhizobia symbiosis Microbiology QR1-502 Carolina A. Contador Siu-Kit Lo Siu H. J. Chan Hon-Ming Lam Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont <named-content content-type="genus-species">Sinorhizobium fredii</named-content> Using Constraint-Based Modeling
description	ABSTRACT Rhizobia are soil bacteria able to establish symbiosis with diverse host plants. Specifically, Sinorhizobium fredii is a soil bacterium that forms nitrogen-fixing root nodules in diverse legumes, including soybean. The strain S. fredii CCBAU45436 is a dominant sublineage of S. fredii that nodulates soybeans in alkaline-saline soils in the Huang-Huai-Hai Plain region of China. Here, we present a manually curated metabolic model of the symbiotic form of Sinorhizobium fredii CCBAU45436. A symbiosis reaction was defined to describe the specific soybean-microsymbiont association. The performance and quality of the reconstruction had a 70% score when assessed using a standardized genome-scale metabolic model test suite. The model was used to evaluate in silico single-gene knockouts to determine the genes controlling the nitrogen fixation process. One hundred forty-one of 541 genes (26%) were found to influence the symbiotic process, wherein 121 genes were predicted as essential and 20 others as having a partial effect. Transcriptomic profiles of CCBAU45436 were used to evaluate the nitrogen fixation capacity in cultivated versus in wild soybean inoculated with the microsymbiont. The model quantified the nitrogen fixation activities of the strain in these two hosts and predicted a higher nitrogen fixation capacity in cultivated soybean. Our results are consistent with published data demonstrating larger amounts of ureides and total nitrogen in cultivated soybean than in wild soybean. This work presents the first metabolic network reconstruction of S. fredii as an example of a useful tool for exploring the potential benefits of microsymbionts to sustainable agriculture and the ecosystem. IMPORTANCE Nitrogen is the most limiting macronutrient for plant growth, and rhizobia are important bacteria for agriculture because they can fix atmospheric nitrogen and make it available to legumes through the establishment of a symbiotic relationship with their host plants. In this work, we studied the nitrogen fixation process in the microsymbiont Sinorhizobium fredii at the genome level. A metabolic model was built using genome annotation and literature to reconstruct the symbiotic form of S. fredii. Genes controlling the nitrogen fixation process were identified by simulating gene knockouts. Additionally, the nitrogen-fixing capacities of S. fredii CCBAU45436 in symbiosis with cultivated and wild soybeans were evaluated. The predictions suggested an outperformance of S. fredii with cultivated soybean, consistent with published experimental evidence. The reconstruction presented here will help to understand and improve nitrogen fixation capabilities of S. fredii and will be beneficial for agriculture by reducing the reliance on fertilizer applications.
format	article
author	Carolina A. Contador Siu-Kit Lo Siu H. J. Chan Hon-Ming Lam
author_facet	Carolina A. Contador Siu-Kit Lo Siu H. J. Chan Hon-Ming Lam
author_sort	Carolina A. Contador
title	Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont <named-content content-type="genus-species">Sinorhizobium fredii</named-content> Using Constraint-Based Modeling
title_short	Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont <named-content content-type="genus-species">Sinorhizobium fredii</named-content> Using Constraint-Based Modeling
title_full	Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont <named-content content-type="genus-species">Sinorhizobium fredii</named-content> Using Constraint-Based Modeling
title_fullStr	Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont <named-content content-type="genus-species">Sinorhizobium fredii</named-content> Using Constraint-Based Modeling
title_full_unstemmed	Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont <named-content content-type="genus-species">Sinorhizobium fredii</named-content> Using Constraint-Based Modeling
title_sort	metabolic analyses of nitrogen fixation in the soybean microsymbiont <named-content content-type="genus-species">sinorhizobium fredii</named-content> using constraint-based modeling
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/f55c39bcb6fa4a77bf055e2e910b5f2a
work_keys_str_mv	AT carolinaacontador metabolicanalysesofnitrogenfixationinthesoybeanmicrosymbiontnamedcontentcontenttypegenusspeciessinorhizobiumfrediinamedcontentusingconstraintbasedmodeling AT siukitlo metabolicanalysesofnitrogenfixationinthesoybeanmicrosymbiontnamedcontentcontenttypegenusspeciessinorhizobiumfrediinamedcontentusingconstraintbasedmodeling AT siuhjchan metabolicanalysesofnitrogenfixationinthesoybeanmicrosymbiontnamedcontentcontenttypegenusspeciessinorhizobiumfrediinamedcontentusingconstraintbasedmodeling AT honminglam metabolicanalysesofnitrogenfixationinthesoybeanmicrosymbiontnamedcontentcontenttypegenusspeciessinorhizobiumfrediinamedcontentusingconstraintbasedmodeling
_version_	1718377776274210816

Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont <named-content content-type="genus-species">Sinorhizobium fredii</named-content> Using Constraint-Based Modeling

Ejemplares similares