Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades
Posted on 2020-01-22 - 08:36
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.
CITE THIS COLLECTION
DataCite
3 Biotech
3D Printing in Medicine
3D Research
3D-Printed Materials and Systems
4OR
AAPG Bulletin
AAPS Open
AAPS PharmSciTech
Abhandlungen aus dem Mathematischen Seminar der Universität Hamburg
ABI Technik (German)
Academic Medicine
Academic Pediatrics
Academic Psychiatry
Academic Questions
Academy of Management Discoveries
Academy of Management Journal
Academy of Management Learning and Education
Academy of Management Perspectives
Academy of Management Proceedings
Academy of Management Review
Abraham, Briana; Caglayan, Deniz; Carrillo, Natalie; Chapman, Matthew; Hagan, Claire; Hansen, Skye; et al. (2020). Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades. figshare. Collection. https://doi.org/10.6084/m9.figshare.c.4825938.v1
or
Select your citation style and then place your mouse over the citation text to select it.
SHARE
Usage metrics
Read the peer-reviewed publication
AUTHORS (27)
BA
Briana Abraham
DC
Deniz Caglayan
NC
Natalie Carrillo
MC
Matthew Chapman
CH
Claire Hagan
SH
Skye Hansen
RJ
Ralph Jeanty
AK
Alexander Klimczak
MK
Marcos Klingler
TK
Thomas Kutcher
SL
Sydney Levy
AM
Angel Millard-Bruzos
TM
Thomas Moore
DP
David Prentice
MP
Matthew Prescott
RR
Richard Roehm
JR
Jordan Rose
MY
Mulan Yin
AH
Ayumi Hyodo
KL
Kathleen Lail