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  • Leaf litter, soil, and periphyton gene expression along freshwater to marine gradients in Everglades National Park (FCE LTER), Florida, USA, January 2021 and April 2021
  • Anderson, Kenneth J; Post-doctoral Scholar; Kent State University
    Kominoski, John S; Associate Professor; Florida International University
    Choi, Chang Jae; Post-doctoral Scholar; University of Florida
    Stingl, Ulrich; Assistant Professor; University of Florida
  • 2024-07-24
  • Anderson, K.J., J.S. Kominoski, C. Choi, and U. Stingl. 2024. Leaf litter, soil, and periphyton gene expression along freshwater to marine gradients in Everglades National Park (FCE LTER), Florida, USA, January 2021 and April 2021 ver 1. Environmental Data Initiative. https://doi.org/DOI_PLACE_HOLDER (Accessed 2024-12-27).

  • We collected leaf litter, periphyton, and soil along freshwater to marine gradients at SRS-2, SRS-4, SRS-6, TS/PH-2, TS/Ph-3, TS/Ph-7a, and TS/Ph-10. Samples were collected in January and April of 2021 to understand how microbial communities respond to and influence the breakdown of organic matter along freshwater to marine transects. Data collection for this project is complete.

    For each site and litter pair we collected a subset of 2-3 g wet mass of litter, a grab sample of soil, and a grab sample of periphyton for each site. All subsamples were preserved at -20°C until extraction, which took place up to a year after initial collection. Samples were sent to Novogene (Novogene Co. Ltd., Beijing, China) for the total RNA extraction followed by metatranscriptome sequencing.

    We selected n = 12 genes/gene families encoding for focal enzymes to investigate which are important to the breakdown of organic matter: Dioxygenases (associated with aerobic respiration), Sulfatases (associated with the release of sulfates from complex molecules), sulfite reductases (associated with sulfite reduction), methyl coenzyme M reductase and formylmethanofuran (associated with methanogenesis), nitrite reductases (associated with nitrite reduction), cellobiosidase, glucosidase, and xylosidase (associated with cellulose breakdown), phenol oxidase (associated with lignin breakdown), acid phosphatase (associated with phosphate acquisition in acidic environments), and alkaline phosphatase (associated with phosphate acquisition in basic environments). For each gene/family of interest, we searched all annotated transcripts for all entries corresponding to that gene/family and combined all values for a total expression.

    We selected n = 6 monophyletic microbial functional groups, representing sulfate reducers, sulfate oxidizers, methane oxidizers, methanogens, nitrite oxidizers, and ammonia oxidizers associated with sulfate and methane cycling. We filtered all annotated transcripts for all species with the following in the name: in the name: ‘desulfo’ for sulfate reducers, ‘sulfito’ for sulfite oxidizers, ‘methylo’ for methyl/methane oxidizers, ‘methano’ for methanogens, ‘nitro’ for nitrite oxidizers, and ‘nitroso’ for aerobic ammonia oxidizers.

  • Geographic Coordinates
    • N: 25.54972811, S: 25.54972811, E: -80.78520692, W: -80.78520692
    • N: 25.40976421, S: 25.40976421, E: -80.96431016, W: -80.96431016
    • N: 25.36462994, S: 25.36462994, E: -81.07794623, W: -81.07794623
    • N: 25.40357188, S: 25.40357188, E: -80.60690341, W: -80.60690341
    • N: 25.25240534, S: 25.25240534, E: -80.66271768, W: -80.66271768
    • N: 25.19080491, S: 25.19080491, E: -80.63910514, W: -80.63910514
    • N: 25.02476744, S: 25.02476744, E: -80.68097374, W: -80.68097374
  • knb-lter-fce.1270.1  (Uploaded 2024-07-24)  
  • This information is released under the Creative Commons license - Attribution - CC BY (https://creativecommons.org/licenses/by/4.0/). The consumer of these data ("Data User" herein) is required to cite it appropriately in any publication that results from its use. The Data User should realize that these data may be actively used by others for ongoing research and that coordination may be necessary to prevent duplicate publication. The Data User is urged to contact the authors of these data if any questions about methodology or results occur. Where appropriate, the Data User is encouraged to consider collaboration or co-authorship with the authors. The Data User should realize that misinterpretation of data may occur if used out of context of the original study. While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy of data sets cannot be guaranteed. All data are made available "as is." The Data User should be aware, however, that data are updated periodically and it is the responsibility of the Data User to check for new versions of the data. The data authors and the repository where these data were obtained shall not be liable for damages resulting from any use or misinterpretation of the data. Thank you.
  • DOI PLACE HOLDER
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