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      Short-Term Transcriptional Response of Microbial Communities to Nitrogen Fertilization in a Pine Forest Soil

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          Abstract

          Ecosystems are receiving increased nitrogen (N) from anthropogenic sources, including fertilizers and emissions from factories and automobiles. High levels of N change ecosystem functioning. For example, high inorganic N decreases the microbial decomposition of plant litter, potentially reducing nutrient recycling for plant growth. Understanding how N regulates microbial decomposition can improve the prediction of ecosystem functioning over extended time scales. We found little support for the conventional view that high N supply represses the expression of genes involved in decomposition or alters the expression of bacterial genes for inorganic N cycling. Instead, our study of pine forest soil 3 days after N addition showed changes in microbial gene expression related to cell maintenance and stress response. This highlights the challenge of establishing predictive links between microbial gene expression levels and measures of ecosystem function.

          ABSTRACT

          Numerous studies have examined the long-term effect of experimental nitrogen (N) deposition in terrestrial ecosystems; however, N-specific mechanistic markers are difficult to disentangle from responses to other environmental changes. The strongest picture of N-responsive mechanistic markers is likely to arise from measurements over a short (hours to days) time scale immediately after inorganic N deposition. Therefore, we assessed the short-term (3-day) transcriptional response of microbial communities in two soil strata from a pine forest to a high dose of N fertilization (ca. 1 mg/g of soil material) in laboratory microcosms. We hypothesized that N fertilization would repress the expression of fungal and bacterial genes linked to N mining from plant litter. However, despite N suppression of microbial respiration, the most pronounced differences in functional gene expression were between strata rather than in response to the N addition. Overall, ∼4% of metabolic genes changed in expression with N addition, while three times as many (∼12%) were significantly different across the different soil strata in the microcosms. In particular, we found little evidence of N changing expression levels of metabolic genes associated with complex carbohydrate degradation (CAZymes) or inorganic N utilization. This suggests that direct N repression of microbial functional gene expression is not the principle mechanism for reduced soil respiration immediately after N deposition. Instead, changes in expression with N addition occurred primarily in general cell maintenance areas, for example, in ribosome-related transcripts. Transcriptional changes in functional gene abundance in response to N addition observed in longer-term field studies likely result from changes in microbial composition.

          IMPORTANCE Ecosystems are receiving increased nitrogen (N) from anthropogenic sources, including fertilizers and emissions from factories and automobiles. High levels of N change ecosystem functioning. For example, high inorganic N decreases the microbial decomposition of plant litter, potentially reducing nutrient recycling for plant growth. Understanding how N regulates microbial decomposition can improve the prediction of ecosystem functioning over extended time scales. We found little support for the conventional view that high N supply represses the expression of genes involved in decomposition or alters the expression of bacterial genes for inorganic N cycling. Instead, our study of pine forest soil 3 days after N addition showed changes in microbial gene expression related to cell maintenance and stress response. This highlights the challenge of establishing predictive links between microbial gene expression levels and measures of ecosystem function.

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          Author and article information

          Contributors
          Role: Editor
          Journal
          Appl Environ Microbiol
          Appl. Environ. Microbiol
          aem
          aem
          AEM
          Applied and Environmental Microbiology
          American Society for Microbiology (1752 N St., N.W., Washington, DC )
          0099-2240
          1098-5336
          25 May 2018
          17 July 2018
          1 August 2018
          : 84
          : 15
          Affiliations
          [a ]Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
          [b ]Department of Environmental Sciences, Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
          Wageningen University
          Author notes
          Address correspondence to Michaeline B. N. Albright, malbright@ 123456lanl.gov .

          Citation Albright MBN, Johansen R, Lopez D, Gallegos-Graves LV, Steven B, Kuske CR, Dunbar J. 2018. Short-term transcriptional response of microbial communities to nitrogen fertilization in a pine forest soil. Appl Environ Microbiol 84:e00598-18. https://doi.org/10.1128/AEM.00598-18.

          Article
          PMC6052259 PMC6052259 6052259 00598-18
          10.1128/AEM.00598-18
          6052259
          29802185
          Copyright © 2018 American Society for Microbiology.
          Page count
          supplementary-material: 1, Figures: 4, Tables: 0, Equations: 0, References: 83, Pages: 13, Words: 8961
          Funding
          Funded by: DOE | SC | Biological and Environmental Research (BER), https://doi.org/10.13039/100006206;
          Award ID: F260LANL2018
          Award Recipient : Award Recipient :
          Funded by: DOE | Office of Science (SC), https://doi.org/10.13039/100006132;
          Award Recipient :
          Categories
          Environmental Microbiology
          Custom metadata
          August 2018

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