ArticleEnvironmental microbiome2020
Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades.
Article in Environmental microbiome, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 27 citations in OpenAlex.
- Article
- Effects of drainage and long-term tillage on greenhouse gas fluxes in a natural wetland: insights from microbial mechanisms.Environmental microbiome · 2025Article
- MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes.mSystems · 2024Article
- Biogeographic patterns and drivers of soil viromes.Nature ecology & evolution · 2024Article
- Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines.Scientific data · 2024Article
- JAMS - A framework for the taxonomic and functional exploration of microbiological genomic data.bioRxiv : the preprint server for biology · 2023Article
- Updated Virophage Taxonomy and Distinction from Polinton-like Viruses.Biomolecules · 2023Article
- Practical Guide to Measuring Wetland Carbon Pools and Fluxes.Wetlands (Wilmington, N.C.) · 2023Review
- De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee.Nature communications · 2022Article
- Functional and Taxonomic Effects of Organic Amendments on the Restoration of Semiarid Quarry Soils.mSystems · 2021Article
- Exploring the Diversity and Aromatic Hydrocarbon Degrading Potential of Epiphytic Fungi on Hornbeams from Chronically Polluted Areas.Journal of fungi (Basel, Switzerland) · 2021Article
- The endophytome (plant-associated microbiome): methodological approaches, biological aspects, and biotech applications.World journal of microbiology & biotechnology · 2021Review
- DOE JGI Metagenome Workflow.mSystems · 2021Article
- Variation in genomic traits of microbial communities among ecosystems.FEMS microbes · 2021Article
Corrections and comments
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Authors and funding
27 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundCurrently, much is unknown about the taxonomic diversity and the mechanisms of methane metabolism in the Florida Everglades ecosystem. The Loxahatchee National Wildlife Refuge is a section of the Florida Everglades that is almost entirely unstudied in regard to taxonomic profiling. This short report analyzes the metagenome of soil samples from this Refuge to investigate the predominant taxa, as well as the abundance of genes involved in environmentally significant metabolic pathways related to methane production (nitrogen fixation and dissimilatory sulfite reduction).
methodsShotgun metagenomic sequencing using the Illumina platform was performed on 17 soil samples from four different sites within the Loxahatchee National Wildlife Refuge, and underwent quality control, assembly, and annotation. The soil from each sample was tested for water content and concentrations of organic carbon and nitrogen.
resultsThe three most common phyla of bacteria for every site were Actinobacteria, Acidobacteria, and Proteobacteria; however, there was variation in relative phylum composition. The most common phylum of Archaea was Euryarchaeota for all sites. Alpha and beta diversity analyses indicated significant congruity in taxonomic diversity in most samples from Sites 1, 3, and 4 and negligible congruity between Site 2 and the other sites. Shotgun metagenomic sequencing revealed the presence of biogeochemical biomarkers of particular interest (e.g., mrcA, nifH, and dsrB) within the samples. The normalized abundances of mcrA, nifH, and dsrB exhibited a positive correlation with nitrogen concentration and water content, and a negative correlation with organic carbon concentration.
conclusionThis Everglades soil metagenomic study allowed examination of wetlands biological processes and showed expected correlations between measured organic constituents and prokaryotic gene frequency. Additionally, the taxonomic profile generated gives a basis for the diversity of prokaryotic microbial life throughout the Everglades.
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