Use of high throughput DNA analysis to characterize the nodule-associated bacterial community from four ages of <i>Inga punctata</i> trees in a Costa Rican cloud forest

William D. Eaton; Debra A. Hamilton; Wen Chen; Alexander Lemenze; Patricia Soteropoulos; William D. Eaton; Debra A. Hamilton; Wen Chen; Alexander Lemenze; Patricia Soteropoulos

doi:10.3934/microbiol.2024027

AIMS Microbiology

2024, Volume 10, Issue 3: 572-595. doi: 10.3934/microbiol.2024027

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Research article

Use of high throughput DNA analysis to characterize the nodule-associated bacterial community from four ages of Inga punctata trees in a Costa Rican cloud forest

1.
Biology Department, Pace University, One Pace Plaza, New York, NY 10038, U.S.A
2.
University for Peace, El Rodeo de Mora, San José, Cd Colón, Costa Rica
3.
Vermont Cooperative Fish and Wildlife Research Unit, Rubenstein School of the Environment and Natural Resources, University of Vermont, Burlington, VT 05405, U.S.A
4.
Monteverde Institute, Puntarenas, Costa Rica
5.
Molecular and Genomics Informatics Core (MaGIC), Rutgers New Jersey Medical School, 205 South Orange Avenue, Newark, NJ 07103, U.S.A
6.
The Genomics Center and Dept of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, 185 South Orange Avenue, MSB F653, Newark, NJ 07103, U.S.A

Received: 13 April 2024 Revised: 25 June 2024 Accepted: 03 July 2024 Published: 23 July 2024

Leguminous tree root nodule nitrogen-fixing bacteria are critical for recuperation of soil C and N cycle processes after disturbance in tropical forests, while other nodule-associated bacteria (NAB) may enhance nodule development and activity, and plant growth. However, little is known of these root nodule microbiomes. Through DNA analysis, we evaluated the bacterial taxa associated with the root nodules of the 1-year-old, 2-year-old, 13-year-old, and old growth Inga punctata trees in a cloud forest. Bradyrhizobium diazoefficiens was the dominant taxon found in all nodules at 63.16% to 85.71% mean percent sequences (MPS) of the total nodule bacterial DNA and was found in the youngest nodules examined (1 year old), suggesting that it is the primary nodular bacteria. There were 26 other NAB genera with collective MPS levels between 7.4% to 12.2%, while 15 of these genera were found in the Bulk Forest soils at collective MPS levels of 4.6%. These bacterial community compositions were different between the NAB and Bulk Forest soils, suggesting the NAB became concentrated within the root nodules, resulting in communities with different compositions from the Bulk Forest soils. Twenty-three of the 26 NAB genera were previously identified with the potential to perform 9 plant growth promoting (PGP) activities, suggesting their importance in root nodule development and plant growth. These NAB communities appeared to successionally develop over time into more complex taxonomic communities, which is consistent with the outcome of advanced microbial communities following succession. The presence of both B. diazoefficiens and the NAB communities in the nodules across all ages of tree roots, and the potential for PGP activities linked with most of the NAB genera, suggest the importance of B. diazoefficiens and the NAB community for nodule development and enhanced development and growth of I. punctata throughout its lifespan, and most critically in the younger plants.
Citation: William D. Eaton, Debra A. Hamilton, Wen Chen, Alexander Lemenze, Patricia Soteropoulos. Use of high throughput DNA analysis to characterize the nodule-associated bacterial community from four ages of Inga punctata trees in a Costa Rican cloud forest[J]. AIMS Microbiology, 2024, 10(3): 572-595. doi: 10.3934/microbiol.2024027

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Abstract

Leguminous tree root nodule nitrogen-fixing bacteria are critical for recuperation of soil C and N cycle processes after disturbance in tropical forests, while other nodule-associated bacteria (NAB) may enhance nodule development and activity, and plant growth. However, little is known of these root nodule microbiomes. Through DNA analysis, we evaluated the bacterial taxa associated with the root nodules of the 1-year-old, 2-year-old, 13-year-old, and old growth Inga punctata trees in a cloud forest. Bradyrhizobium diazoefficiens was the dominant taxon found in all nodules at 63.16% to 85.71% mean percent sequences (MPS) of the total nodule bacterial DNA and was found in the youngest nodules examined (1 year old), suggesting that it is the primary nodular bacteria. There were 26 other NAB genera with collective MPS levels between 7.4% to 12.2%, while 15 of these genera were found in the Bulk Forest soils at collective MPS levels of 4.6%. These bacterial community compositions were different between the NAB and Bulk Forest soils, suggesting the NAB became concentrated within the root nodules, resulting in communities with different compositions from the Bulk Forest soils. Twenty-three of the 26 NAB genera were previously identified with the potential to perform 9 plant growth promoting (PGP) activities, suggesting their importance in root nodule development and plant growth. These NAB communities appeared to successionally develop over time into more complex taxonomic communities, which is consistent with the outcome of advanced microbial communities following succession. The presence of both B. diazoefficiens and the NAB communities in the nodules across all ages of tree roots, and the potential for PGP activities linked with most of the NAB genera, suggest the importance of B. diazoefficiens and the NAB community for nodule development and enhanced development and growth of I. punctata throughout its lifespan, and most critically in the younger plants.

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