Varying microbial utilization of straw-derived carbon with different long-term fertilization regimes explored by DNA stable-isotope probing

2022 ◽  
Vol 108 ◽  
pp. 103379
Author(s):  
Tengfei Guo ◽  
Qian Zhang ◽  
Dali Song ◽  
Chao Ai ◽  
Shuiqing Zhang ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Stable Isotope Probing ◽  
Microbial Utilization

Microbial utilization of rice root residue‐derived carbon explored by DNA stable‐isotope probing

2020 ◽  
Vol 72 (1) ◽  
pp. 460-473
Author(s):  
Tengfei Guo ◽  
Qian Zhang ◽  
Chao Ai ◽  
Ping He ◽  
Wei Zhou
Keyword(s):  
Stable Isotope ◽  
Stable Isotope Probing ◽  
Rice Root ◽  
Microbial Utilization

scholarly journals Long-Term Enrichment of Stress-Tolerant Cellulolytic Soil Populations following Timber Harvesting Evidenced by Multi-Omic Stable Isotope Probing

2017 ◽  
Vol 8 ◽  
Author(s):  
Roland C. Wilhelm ◽  
Erick Cardenas ◽  
Hilary Leung ◽  
András Szeitz ◽  
Lionel D. Jensen ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Timber Harvesting ◽  
Stable Isotope Probing ◽  
Term Enrichment

scholarly journals Active Soil Nitrifying Communities Revealed by In Situ Transcriptomics and Microcosm-Based Stable-Isotope Probing

2020 ◽  
Vol 86 (23) ◽  
Author(s):  
Wei-Wei Xia ◽  
Jun Zhao ◽  
Yan Zheng ◽  
Hui-Min Zhang ◽  
Jia-Bao Zhang ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Stable Isotope Probing ◽  
Field Conditions ◽  
Nitrogen Fertilizers ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Content Type ◽  
Nitrite Oxidizing Bacteria

ABSTRACT Long-term nitrogen field fertilization often results in significant changes in nitrifying communities that catalyze a key step in the global N cycle. However, whether microcosm studies are able to inform the dynamic changes in communities of ammonia-oxidizing bacteria (AOB) and archaea (AOA) under field conditions remains poorly understood. This study aimed to evaluate the transcriptional activities of nitrifying communities under in situ conditions, and we found that they were largely similar to those of 13C-labeled nitrifying communities in the urea-amended microcosms of soils that had received different N fertilization regimens for 22 years. High-throughput sequencing of 16S rRNA genes and transcripts suggested that Nitrosospira cluster 3-like AOB and Nitrososphaera viennensis-like AOA were significantly stimulated in N-fertilized fresh soils. Real-time quantitative PCR demonstrated that the significant increase of AOA and AOB in fresh soils upon nitrogen fertilization could be preserved in the air-dried soils. DNA-based stable-isotope probing (SIP) further revealed the greatest labeling of Nitrosospira cluster 3-like AOB and Nitrosospira viennensis-like AOA, despite the strong advantage of AOB over AOA in the N-fertilized soils. Nitrobacter-like nitrite-oxidizing bacteria (NOB) played more important roles than Nitrospira-like NOB in urea-amended SIP microcosms, while the situation was the opposite under field conditions. Our results suggest that long-term fertilization selected for physiologically versatile AOB and AOA that could have been adapted to a wide range of substrate ammonium concentrations. It also provides compelling evidence that the dominant communities of transcriptionally active nitrifiers under field conditions were largely similar to those revealed in 13C-labeled microcosms. IMPORTANCE The role of manipulated microcosms in microbial ecology has been much debated, because they cannot entirely represent the in situ situation. We collected soil samples from 20 field plots, including 5 different treatments with and without nitrogen fertilizers for 22 years, in order to assess active nitrifying communities by in situ transcriptomics and microcosm-based stable-isotope probing. The results showed that chronic N enrichment led to competitive advantages of Nitrosospira cluster 3-like AOB over N. viennensis-like AOA in soils under field conditions. Microcosm labeling revealed similar results for active AOA and AOB, although an apparent discrepancy was observed for nitrite-oxidizing bacteria. This study suggests that the soil microbiome represents a relatively stable community resulting from complex evolutionary processes over a large time scale, and microcosms can serve as powerful tools to test the theory of environmental filtering on the key functional microbial guilds.

scholarly journals 13C-Carrier DNA Shortens the Incubation Time Needed To Detect Benzoate-Utilizing Denitrifying Bacteria by Stable-Isotope Probing

2005 ◽  
Vol 71 (9) ◽  
pp. 5192-5196 ◽  
Author(s):  
E. Gallagher ◽  
L. McGuinness ◽  
C. Phelps ◽  
L. Y. Young ◽  
L. J. Kerkhof
Keyword(s):  
Stable Isotope ◽  
Incubation Time ◽  
Bacterial Population ◽  
Temporal Analysis ◽  
Stable Isotope Probing ◽  
Coastal Sediments ◽  
Bacterial Dna ◽  
Gradient Separation ◽  
Density Gradient Separation

ABSTRACT The active bacterial community able to utilize benzoate under denitrifying conditions was elucidated in two coastal sediments using stable-isotope probing (SIP) and nosZ gene amplification. The SIP method employed samples from Norfolk Harbor, Virginia, and a Long-Term Ecosystem Observatory (no. 15) off the coast of Tuckerton, New Jersey. The SIP method was modified by use of archaeal carrier DNA in the density gradient separation. The carrier DNA significantly reduced the incubation time necessary to detect the 13C-labeled bacterial DNA from weeks to hours in the coastal enrichments. No denitrifier DNA was found to contaminate the archaeal 13C-carrier when [12C]benzoate was used as a substrate in the sediment enrichments. Shifts in the activity of the benzoate-utilizing denitrifying population could be detected throughout a 21-day incubation. These results suggest that temporal analysis using SIP can be used to illustrate the initial biodegrader(s) in a bacterial population and to document the cross-feeding microbial community.

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