Transcriptome analysis of nitrogen assimilation preferences in Burkholderia sp. M6-3 and Arthrobacter sp. M7-15
IntroductionAmmonium (NH4+) and nitrate (NO3−) are the two main forms of inorganic nitrogen (N) that exist in soil and both can be absorbed and utilized by plants. As a vast and crucial biome, soil microorganisms are responsible for mediating the inorganic N assimilation process and enhancing nitrog...
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Frontiers Media S.A.
2025-04-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1559884/full |
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| author | Ran Liu Ran Liu Hongyi Qin Qian Wang Cheng Chu Yunbin Jiang Huan Deng Cheng Han Cheng Han Wenhui Zhong Wenhui Zhong Wenhui Zhong |
| author_facet | Ran Liu Ran Liu Hongyi Qin Qian Wang Cheng Chu Yunbin Jiang Huan Deng Cheng Han Cheng Han Wenhui Zhong Wenhui Zhong Wenhui Zhong |
| author_sort | Ran Liu |
| collection | DOAJ |
| description | IntroductionAmmonium (NH4+) and nitrate (NO3−) are the two main forms of inorganic nitrogen (N) that exist in soil and both can be absorbed and utilized by plants. As a vast and crucial biome, soil microorganisms are responsible for mediating the inorganic N assimilation process and enhancing nitrogen use efficiency. Understanding how these microorganisms assimilate different forms of inorganic nitrogen is crucial. There are a handful of microorganisms that play a dominant role in the process of soil inorganic nitrogen assimilation and have a significant advantage in abundance. However, microbial preferences for ammonium or nitrate, as well as differences in their metabolic pathways under co-existing ammonium and nitrate conditions, remain unclear.MethodsIn this study, two microbial strains with nitrogen assimilation advantages, Burkholderia sp. M6-3 and Arthrobacter sp. M7-15 were isolated from an acidic Chinese soil and then incubated by different sources of inorganic N to investigate their N preferences. Furthermore, RNA sequencing-based transcriptome analysis was used to map the metabolic pathways of the two strains and explore their explanatory potential for N preferences.ResultsThe results showed that strain M6-3 preferred to utilize NH4+ while strain M7-15 preferred to utilize NO3−. Although both strains shared similar nitrogen metabolic pathways, the differential expression of the glutamine synthetase-coding gene glnA played a crucial role in regulating their inorganic N preferences. This inconsistency in glnA expression may be attributed to GlnR, a global regulator of nitrogen utilization.DiscussionThis research strengthens the theoretical basis for exploring the underlying causes of differential preferences for inorganic N forms and provided key clues for screening functional microorganisms to ultimately enhance inorganic nitrogen use efficiency. |
| format | Article |
| id | doaj-art-13bb7db7e19b4575933ac98bdf731428 |
| institution | OA Journals |
| issn | 1664-302X |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Microbiology |
| spelling | doaj-art-13bb7db7e19b4575933ac98bdf7314282025-08-20T02:08:47ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2025-04-011610.3389/fmicb.2025.15598841559884Transcriptome analysis of nitrogen assimilation preferences in Burkholderia sp. M6-3 and Arthrobacter sp. M7-15Ran Liu0Ran Liu1Hongyi Qin2Qian Wang3Cheng Chu4Yunbin Jiang5Huan Deng6Cheng Han7Cheng Han8Wenhui Zhong9Wenhui Zhong10Wenhui Zhong11College of Zhongbei, Nanjing Normal University, Danyang, Jiangsu, ChinaJiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, School of Geographical Sciences, Nanjing Normal University, Nanjing, ChinaCollege of Zhongbei, Nanjing Normal University, Danyang, Jiangsu, ChinaJiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, School of Geographical Sciences, Nanjing Normal University, Nanjing, ChinaCollege of Zhongbei, Nanjing Normal University, Danyang, Jiangsu, ChinaJiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, School of Geographical Sciences, Nanjing Normal University, Nanjing, ChinaSchool of Environment, Nanjing Normal University, Nanjing, ChinaJiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, School of Geographical Sciences, Nanjing Normal University, Nanjing, ChinaJiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, ChinaCollege of Zhongbei, Nanjing Normal University, Danyang, Jiangsu, ChinaJiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, School of Geographical Sciences, Nanjing Normal University, Nanjing, ChinaJiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, ChinaIntroductionAmmonium (NH4+) and nitrate (NO3−) are the two main forms of inorganic nitrogen (N) that exist in soil and both can be absorbed and utilized by plants. As a vast and crucial biome, soil microorganisms are responsible for mediating the inorganic N assimilation process and enhancing nitrogen use efficiency. Understanding how these microorganisms assimilate different forms of inorganic nitrogen is crucial. There are a handful of microorganisms that play a dominant role in the process of soil inorganic nitrogen assimilation and have a significant advantage in abundance. However, microbial preferences for ammonium or nitrate, as well as differences in their metabolic pathways under co-existing ammonium and nitrate conditions, remain unclear.MethodsIn this study, two microbial strains with nitrogen assimilation advantages, Burkholderia sp. M6-3 and Arthrobacter sp. M7-15 were isolated from an acidic Chinese soil and then incubated by different sources of inorganic N to investigate their N preferences. Furthermore, RNA sequencing-based transcriptome analysis was used to map the metabolic pathways of the two strains and explore their explanatory potential for N preferences.ResultsThe results showed that strain M6-3 preferred to utilize NH4+ while strain M7-15 preferred to utilize NO3−. Although both strains shared similar nitrogen metabolic pathways, the differential expression of the glutamine synthetase-coding gene glnA played a crucial role in regulating their inorganic N preferences. This inconsistency in glnA expression may be attributed to GlnR, a global regulator of nitrogen utilization.DiscussionThis research strengthens the theoretical basis for exploring the underlying causes of differential preferences for inorganic N forms and provided key clues for screening functional microorganisms to ultimately enhance inorganic nitrogen use efficiency.https://www.frontiersin.org/articles/10.3389/fmicb.2025.1559884/fullinorganic nitrogen assimilationnitrogen preferencebacterial strainsRNA-seq analysisnitrogen metabolic pathway |
| spellingShingle | Ran Liu Ran Liu Hongyi Qin Qian Wang Cheng Chu Yunbin Jiang Huan Deng Cheng Han Cheng Han Wenhui Zhong Wenhui Zhong Wenhui Zhong Transcriptome analysis of nitrogen assimilation preferences in Burkholderia sp. M6-3 and Arthrobacter sp. M7-15 Frontiers in Microbiology inorganic nitrogen assimilation nitrogen preference bacterial strains RNA-seq analysis nitrogen metabolic pathway |
| title | Transcriptome analysis of nitrogen assimilation preferences in Burkholderia sp. M6-3 and Arthrobacter sp. M7-15 |
| title_full | Transcriptome analysis of nitrogen assimilation preferences in Burkholderia sp. M6-3 and Arthrobacter sp. M7-15 |
| title_fullStr | Transcriptome analysis of nitrogen assimilation preferences in Burkholderia sp. M6-3 and Arthrobacter sp. M7-15 |
| title_full_unstemmed | Transcriptome analysis of nitrogen assimilation preferences in Burkholderia sp. M6-3 and Arthrobacter sp. M7-15 |
| title_short | Transcriptome analysis of nitrogen assimilation preferences in Burkholderia sp. M6-3 and Arthrobacter sp. M7-15 |
| title_sort | transcriptome analysis of nitrogen assimilation preferences in burkholderia sp m6 3 and arthrobacter sp m7 15 |
| topic | inorganic nitrogen assimilation nitrogen preference bacterial strains RNA-seq analysis nitrogen metabolic pathway |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1559884/full |
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