Domesticated rice alters the rhizosphere microbiome, reducing nitrogen fixation and increasing nitrous oxide emissions

Crop domestication has revolutionized food production but increased agriculture’s reliance on fertilizers and pesticides. We investigate differences in the rhizosphere microbiome functions of wild and domesticated rice, focusing on nitrogen (N) cycling genes. Shotgun metagenomics and real-time PCR r...

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Published inNature communications Vol. 16; no. 1; pp. 2038 - 14
Main Authors Chang, Jingjing, Costa, Ohana Y. A., Sun, Yu, Wang, Jilin, Tian, Lei, Shi, Shaohua, Wang, Enze, Ji, Li, Wang, Changji, Pang, Yingnan, Yao, Zongmu, Ye, Libo, Zhang, Jianfeng, Chen, Hongping, Cai, Yaohui, Chen, Dazhou, Song, Zhiping, Rong, Jun, Raaijmakers, Jos M., Tian, Chunjie, Kuramae, Eiko E.
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 27.02.2025
Nature Publishing Group
Nature Portfolio
Subjects
45/22
45/23
45/41
45/77
631/326/2565/855
704/158/2456
704/844/685
Abundance
Agrochemicals
Bacteria
Bacteria - genetics
Bacteria - metabolism
Crops
Domestication
Emission measurements
Emissions
Exudates
Fertilizers
Food
Food production
Genes
Greenhouse gases
Humanities and Social Sciences
Metabolites
Metabolomics
Metagenomics
Microbiomes
Microbiota - genetics
Microorganisms
multidisciplinary
Nitrogen
Nitrogen - metabolism
Nitrogen fixation
Nitrogen Fixation - genetics
Nitrogenase
Nitrogenase - genetics
Nitrogenase - metabolism
Nitrogenation
Nitrous oxide
Nitrous Oxide - metabolism
Oryza - genetics
Oryza - metabolism
Oryza - microbiology
Pesticides
Plant Roots - metabolism
Plant Roots - microbiology
Real time
Rhizosphere
Rice
Science
Science (multidisciplinary)
Soil - chemistry
Soil Microbiology
Soils
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Abstract Crop domestication has revolutionized food production but increased agriculture’s reliance on fertilizers and pesticides. We investigate differences in the rhizosphere microbiome functions of wild and domesticated rice, focusing on nitrogen (N) cycling genes. Shotgun metagenomics and real-time PCR reveal a higher abundance of N-fixing genes in the wild rice rhizosphere microbiomes. Validation through transplanting rhizosphere microbiome suspensions shows the highest nitrogenase activity in soils with wild rice suspensions, regardless of planted rice type. Domesticated rice, however, exhibits an increased number of genes associated with nitrous oxide (N 2 O) production. Measurements of N 2 O emissions in soils with wild and domesticated rice are significantly higher in soil with domesticated rice compared to wild rice. Comparative root metabolomics between wild and domesticated rice further show that wild rice root exudates positively correlate with the frequency and abundance of microbial N-fixing genes, as indicated by metagenomic and qPCR, respectively. To confirm, we add wild and domesticated rice root metabolites to black soil, and qPCR shows that wild rice exudates maximize microbial N-fixing gene abundances and nitrogenase activity. Collectively, these findings suggest that rice domestication negatively impacts N-fixing bacteria and enriches bacteria that produce the greenhouse gas N 2 O, highlighting the environmental trade-offs associated with crop domestication. Domestication of crops has boosted food production but increased dependence on fertilizers and pesticides. This study shows that wild rice harbors a higher abundance of nitrogen-fixing genes in the rhizosphere, while domesticated rice has more genes associated with nitrous oxide production.
AbstractList Abstract Crop domestication has revolutionized food production but increased agriculture’s reliance on fertilizers and pesticides. We investigate differences in the rhizosphere microbiome functions of wild and domesticated rice, focusing on nitrogen (N) cycling genes. Shotgun metagenomics and real-time PCR reveal a higher abundance of N-fixing genes in the wild rice rhizosphere microbiomes. Validation through transplanting rhizosphere microbiome suspensions shows the highest nitrogenase activity in soils with wild rice suspensions, regardless of planted rice type. Domesticated rice, however, exhibits an increased number of genes associated with nitrous oxide (N2O) production. Measurements of N2O emissions in soils with wild and domesticated rice are significantly higher in soil with domesticated rice compared to wild rice. Comparative root metabolomics between wild and domesticated rice further show that wild rice root exudates positively correlate with the frequency and abundance of microbial N-fixing genes, as indicated by metagenomic and qPCR, respectively. To confirm, we add wild and domesticated rice root metabolites to black soil, and qPCR shows that wild rice exudates maximize microbial N-fixing gene abundances and nitrogenase activity. Collectively, these findings suggest that rice domestication negatively impacts N-fixing bacteria and enriches bacteria that produce the greenhouse gas N2O, highlighting the environmental trade-offs associated with crop domestication.
Crop domestication has revolutionized food production but increased agriculture’s reliance on fertilizers and pesticides. We investigate differences in the rhizosphere microbiome functions of wild and domesticated rice, focusing on nitrogen (N) cycling genes. Shotgun metagenomics and real-time PCR reveal a higher abundance of N-fixing genes in the wild rice rhizosphere microbiomes. Validation through transplanting rhizosphere microbiome suspensions shows the highest nitrogenase activity in soils with wild rice suspensions, regardless of planted rice type. Domesticated rice, however, exhibits an increased number of genes associated with nitrous oxide (N2O) production. Measurements of N2O emissions in soils with wild and domesticated rice are significantly higher in soil with domesticated rice compared to wild rice. Comparative root metabolomics between wild and domesticated rice further show that wild rice root exudates positively correlate with the frequency and abundance of microbial N-fixing genes, as indicated by metagenomic and qPCR, respectively. To confirm, we add wild and domesticated rice root metabolites to black soil, and qPCR shows that wild rice exudates maximize microbial N-fixing gene abundances and nitrogenase activity. Collectively, these findings suggest that rice domestication negatively impacts N-fixing bacteria and enriches bacteria that produce the greenhouse gas N2O, highlighting the environmental trade-offs associated with crop domestication.Domestication of crops has boosted food production but increased dependence on fertilizers and pesticides. This study shows that wild rice harbors a higher abundance of nitrogen-fixing genes in the rhizosphere, while domesticated rice has more genes associated with nitrous oxide production.
Crop domestication has revolutionized food production but increased agriculture’s reliance on fertilizers and pesticides. We investigate differences in the rhizosphere microbiome functions of wild and domesticated rice, focusing on nitrogen (N) cycling genes. Shotgun metagenomics and real-time PCR reveal a higher abundance of N-fixing genes in the wild rice rhizosphere microbiomes. Validation through transplanting rhizosphere microbiome suspensions shows the highest nitrogenase activity in soils with wild rice suspensions, regardless of planted rice type. Domesticated rice, however, exhibits an increased number of genes associated with nitrous oxide (N 2 O) production. Measurements of N 2 O emissions in soils with wild and domesticated rice are significantly higher in soil with domesticated rice compared to wild rice. Comparative root metabolomics between wild and domesticated rice further show that wild rice root exudates positively correlate with the frequency and abundance of microbial N-fixing genes, as indicated by metagenomic and qPCR, respectively. To confirm, we add wild and domesticated rice root metabolites to black soil, and qPCR shows that wild rice exudates maximize microbial N-fixing gene abundances and nitrogenase activity. Collectively, these findings suggest that rice domestication negatively impacts N-fixing bacteria and enriches bacteria that produce the greenhouse gas N 2 O, highlighting the environmental trade-offs associated with crop domestication. Domestication of crops has boosted food production but increased dependence on fertilizers and pesticides. This study shows that wild rice harbors a higher abundance of nitrogen-fixing genes in the rhizosphere, while domesticated rice has more genes associated with nitrous oxide production.
Crop domestication has revolutionized food production but increased agriculture's reliance on fertilizers and pesticides. We investigate differences in the rhizosphere microbiome functions of wild and domesticated rice, focusing on nitrogen (N) cycling genes. Shotgun metagenomics and real-time PCR reveal a higher abundance of N-fixing genes in the wild rice rhizosphere microbiomes. Validation through transplanting rhizosphere microbiome suspensions shows the highest nitrogenase activity in soils with wild rice suspensions, regardless of planted rice type. Domesticated rice, however, exhibits an increased number of genes associated with nitrous oxide (N2O) production. Measurements of N2O emissions in soils with wild and domesticated rice are significantly higher in soil with domesticated rice compared to wild rice. Comparative root metabolomics between wild and domesticated rice further show that wild rice root exudates positively correlate with the frequency and abundance of microbial N-fixing genes, as indicated by metagenomic and qPCR, respectively. To confirm, we add wild and domesticated rice root metabolites to black soil, and qPCR shows that wild rice exudates maximize microbial N-fixing gene abundances and nitrogenase activity. Collectively, these findings suggest that rice domestication negatively impacts N-fixing bacteria and enriches bacteria that produce the greenhouse gas N2O, highlighting the environmental trade-offs associated with crop domestication.Crop domestication has revolutionized food production but increased agriculture's reliance on fertilizers and pesticides. We investigate differences in the rhizosphere microbiome functions of wild and domesticated rice, focusing on nitrogen (N) cycling genes. Shotgun metagenomics and real-time PCR reveal a higher abundance of N-fixing genes in the wild rice rhizosphere microbiomes. Validation through transplanting rhizosphere microbiome suspensions shows the highest nitrogenase activity in soils with wild rice suspensions, regardless of planted rice type. Domesticated rice, however, exhibits an increased number of genes associated with nitrous oxide (N2O) production. Measurements of N2O emissions in soils with wild and domesticated rice are significantly higher in soil with domesticated rice compared to wild rice. Comparative root metabolomics between wild and domesticated rice further show that wild rice root exudates positively correlate with the frequency and abundance of microbial N-fixing genes, as indicated by metagenomic and qPCR, respectively. To confirm, we add wild and domesticated rice root metabolites to black soil, and qPCR shows that wild rice exudates maximize microbial N-fixing gene abundances and nitrogenase activity. Collectively, these findings suggest that rice domestication negatively impacts N-fixing bacteria and enriches bacteria that produce the greenhouse gas N2O, highlighting the environmental trade-offs associated with crop domestication.
Crop domestication has revolutionized food production but increased agriculture's reliance on fertilizers and pesticides. We investigate differences in the rhizosphere microbiome functions of wild and domesticated rice, focusing on nitrogen (N) cycling genes. Shotgun metagenomics and real-time PCR reveal a higher abundance of N-fixing genes in the wild rice rhizosphere microbiomes. Validation through transplanting rhizosphere microbiome suspensions shows the highest nitrogenase activity in soils with wild rice suspensions, regardless of planted rice type. Domesticated rice, however, exhibits an increased number of genes associated with nitrous oxide (N O) production. Measurements of N O emissions in soils with wild and domesticated rice are significantly higher in soil with domesticated rice compared to wild rice. Comparative root metabolomics between wild and domesticated rice further show that wild rice root exudates positively correlate with the frequency and abundance of microbial N-fixing genes, as indicated by metagenomic and qPCR, respectively. To confirm, we add wild and domesticated rice root metabolites to black soil, and qPCR shows that wild rice exudates maximize microbial N-fixing gene abundances and nitrogenase activity. Collectively, these findings suggest that rice domestication negatively impacts N-fixing bacteria and enriches bacteria that produce the greenhouse gas N O, highlighting the environmental trade-offs associated with crop domestication.
ArticleNumber 2038
Author Rong, Jun
Song, Zhiping
Wang, Jilin
Pang, Yingnan
Tian, Chunjie
Tian, Lei
Wang, Changji
Chen, Dazhou
Yao, Zongmu
Ye, Libo
Raaijmakers, Jos M.
Cai, Yaohui
Sun, Yu
Ji, Li
Chang, Jingjing
Wang, Enze
Zhang, Jianfeng
Shi, Shaohua
Chen, Hongping
Costa, Ohana Y. A.
Kuramae, Eiko E.
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/40016229$$D View this record in MEDLINE/PubMed
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Snippet Crop domestication has revolutionized food production but increased agriculture’s reliance on fertilizers and pesticides. We investigate differences in the...
Crop domestication has revolutionized food production but increased agriculture's reliance on fertilizers and pesticides. We investigate differences in the...
Abstract Crop domestication has revolutionized food production but increased agriculture’s reliance on fertilizers and pesticides. We investigate differences...
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SubjectTerms 45/22
45/23
45/41
45/77
631/326/2565/855
704/158/2456
704/844/685
Abundance
Agrochemicals
Bacteria
Bacteria - genetics
Bacteria - metabolism
Crops
Domestication
Emission measurements
Emissions
Exudates
Fertilizers
Food
Food production
Genes
Greenhouse gases
Humanities and Social Sciences
Metabolites
Metabolomics
Metagenomics
Microbiomes
Microbiota - genetics
Microorganisms
multidisciplinary
Nitrogen
Nitrogen - metabolism
Nitrogen fixation
Nitrogen Fixation - genetics
Nitrogenase
Nitrogenase - genetics
Nitrogenase - metabolism
Nitrogenation
Nitrous oxide
Nitrous Oxide - metabolism
Oryza - genetics
Oryza - metabolism
Oryza - microbiology
Pesticides
Plant Roots - metabolism
Plant Roots - microbiology
Real time
Rhizosphere
Rice
Science
Science (multidisciplinary)
Soil - chemistry
Soil Microbiology
Soils
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Title Domesticated rice alters the rhizosphere microbiome, reducing nitrogen fixation and increasing nitrous oxide emissions
URI https://link.springer.com/article/10.1038/s41467-025-57213-x
https://www.ncbi.nlm.nih.gov/pubmed/40016229
https://www.proquest.com/docview/3171986189
https://www.proquest.com/docview/3172268936
https://doaj.org/article/d528d99dc6bb4caba479c432418d4853
Volume 16
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