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

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

Observation of a Novel PFOS-Precursor, the Perfluorooctane Sulfonamido Ethanol-Based Phosphate (SAmPAP) Diester, in Marine Sediments

The environmental occurrence of perfluorooctane sulfonate (PFOS) can arise from its direct use as well as from transformation of precursors ((<i>N</i>-alkyl substituted) perfluorooctane sulfonamides; FOSAMs). Perfluorooctane sulfonamidoethanol-based phosphate (SAmPAP) esters are among numerous potential PFOS-precursors which have not been previously detected in the environment and for which little is known about their stability. Based on their high production volume during the 1970s–2002 and widespread use in food contact paper and packaging, SAmPAP esters may be potentially significant sources of PFOS. Here we report for the first time on the environmental occurrence of SAmPAP diester in marine sediments from an urbanized marine harbor in Vancouver, Canada. SAmPAP diester concentrations in sediment (40–200 pg/g dry weight) were similar to those of PFOS (71–180 pg/g). A significant (<i>p</i> < 0.05) correlation was observed between SAmPAP diester and <i>N</i>-ethyl perfluorooctane sulfonamido acetate (an anticipated degradation product of SAmPAP diester). ∑PFOS-precursor (FOSAM) concentrations in sediment (120–1100 pg/g) were 1.6–24 times greater than those of PFOS in sediment. Although SAmPAP diester was not detected in water, PFOS was observed at concentrations up to 710 pg/L. Among the per- and polyfluoroalkyl substances monitored in the present work, mean log-transformed sediment/water distribution coefficients ranged from 2.3 to 4.3 and increased with number of CF₂ units and N-alkyl substitution (in the case of FOSAMs). Overall, these results highlight the importance of FOSAMs as potentially significant sources of PFOS, in particular for urban marine environments

Biodegradation of <i>N</i>‑Ethyl Perfluorooctane Sulfonamido Ethanol (EtFOSE) and EtFOSE-Based Phosphate Diester (SAmPAP Diester) in Marine Sediments

Investigations into the biodegradation potential of perfluorooctane sulfonate (PFOS)-precursor candidates have focused on low molecular weight substances (e.g., <i>N</i>-ethyl perfluorooctane sulfonamido ethanol (EtFOSE)) in wastewater treatment plant sludge. Few data are available on PFOS-precursor biodegradation in other environmental compartments, and nothing is known about the stability of high-molecular-weight perfluorooctane sulfonamide-based substances such as the EtFOSE-based phosphate diester (SAmPAP diester) in any environmental compartment. In the present work, the biodegradation potential of SAmPAP diester and EtFOSE by bacteria in marine sediments was evaluated over 120 days at 4 and 25 °C. At both temperatures, EtFOSE was transformed to a suite of products, including <i>N</i>-ethyl perfluorooctane sulfonamidoacetate, perfluorooctane sulfonamidoacetate, <i>N</i>-ethyl perfluorooctane sulfonamide, perfluorooctane sulfonamide, and perfluorooctane sulfonate. Transformation was significantly more rapid at 25 °C (<i>t</i>_1/2 = 44 ± 3.4 days; error represents standard error of the mean (SEM)) compared to 4 °C (<i>t</i>_1/2 = 160 ± 17 days), but much longer than previous biodegradation studies involving EtFOSE in sludge (<i>t</i>_1/2 ∼0.7–4.2 days). In contrast, SAmPAP diester was highly recalcitrant to microbial degradation, with negligible loss and/or associated product formation observed after 120 days at both temperatures, and an estimated half-life of >380 days at 25 °C (estimated using the lower bounds 95% confidence interval of the slope). We hypothesize that the hydrophobicity of SAmPAP diester reduces its bioavailability, thus limiting biotransformation by bacteria in sediments. The lengthy biodegradation half-life of EtFOSE and recalcitrant nature of SAmPAP diester in part explains the elevated concentrations of PFOS-precursors observed in urban marine sediments from Canada, Japan, and the U.S, over a decade after phase-out of their production and commercial application in these countries

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

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