Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades

Abstract

Background: Currently, 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). Methods: Shotgun 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. Results: The 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. Conclusion: This 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.

Metagenomes from the Loxahatchee wildlife refuge in the Florida Everglades

“…The mcrA gene is a marker gene involved in the methane metabolism pathway. A positive correlation between the nitrogen concentration and the gene frequency of mcrA, as well as a negative correlation with carbon concentration, have been observed in the wetland's soil 2 . This suggests potential correlations between the abundance of the mcrA gene and the aquatic carbon and nitrogen concentrations.…”

“…The Arthur R. Marshall Loxahatchee National Wildlife Refuge encompasses 585 km 2 of land in the Florida Everglades that has remained relatively undisturbed due to limited anthropogenic influences 1 . Agricultural fields dominate the Northern and Western sides of the refuge while the Eastern side is primarily bordered by urban development.…”

“…Previously, we applied shotgun metagenome sequencing to wetland soil samples collected across four sites within the Loxahatchee Refuge to investigate microbiome diversity and biogeochemically-relevant microbial processes 2 . In this report, we expand upon our initial study by collecting submerged sediment and water samples from the north, south, east and west sides of the refuge (Fig.…”

“…In this report, we expand upon our initial study by collecting submerged sediment and water samples from the north, south, east and west sides of the refuge (Fig. 1b) to investigate (1) how location-specific environmental factors may contribute to differences in taxonomic diversity, (2) if potentially unique metagenome-assembled genomes (MAGs) can be assembled from sediment samples taken from the refuge, and (3) how environmental factors may impact the prevalence of genes related to energy cycling. Following sediment and water collection, DNA from the sediment samples was extracted, sequenced, assembled, and annotated.…”

The DOE JGI Metagenome Workflow

“…The workflow performs multiple quality checks and artifact removal, and provides a variety of summary statistics to assist users with the assessment of data quality and consistency. We illustrate the workflow using microbiomes from the Loxahatchee Nature Preserve in the Florida Everglades(8) as an example. In this follow-up study, sediment samples were collected and DNA was isolated by the students of Boca Raton Community High School, Boca Raton, from 4 different sites in the Loxahatchee Nature Preserve with 5 replicates at each site as previously described.…”