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

Briana S Abraham,David J Prentice,Jonathan B Benskin,Christopher Daum,Matthew C Chapman,Matthew E Prescott,Thomas B Moore,Jordan A Rose,Alexander A Klimczak,Ayumi Hyodo,Kathleen Lail,Skye T Hansen,Richard Roehm,Rekha Seshadri,Ralph O Jeanty,Alex Copeland,Claire T Hagan,Tijana Glavina Del Rio,Thomas P Kutcher,Marcos J Klingler,Emiley A Eloe‐Fadrosh ,Deniz Caglayan,Mulan Yin,Angel A Millard-Bruzos,Sydney H Levy,Natalie V Carrillo,Alicia Clum

doi:10.1186/s40793-019-0352-4

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.

Highlights

Much is unknown about the taxonomic diversity and the mechanisms of methane metabolism in the Florida Everglades ecosystem
The three most dominant bacterial phyla among all three sites were Proteobacteria, Acidobacteria, and Actinobacteria, which have been reported as common soil microorganisms (Fig. 2a) [7]
These results correspond to previous research that has suggested that nifH gene abundance is primarily impacted by factors including nitrogen concentration and microbial biomass carbon, while the negative correlation with total carbon is supported by findings that low organic matter and high microbial biomass are ideal for the presence of nifH [13]

Summary

Introduction

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). Previous studies within the Florida Everglades ecosystem have focused on the distribution and activity of methanogens in relation to methane cycling and emissions in the Water Conservation Area 2A (WCA-2A) [3, 4] This site has experienced significant annual agricultural runoff over the past several years, resulting in a more nitrogen-limited system with an excess of phosphorous and concomitant changes in the overall microbial assemblages. The Loxahatchee Refuge represents an accessible and unperturbed system to investigate microbiome diversity and biogeochemically-relevant microbial processes

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Conclusion