Fine grained compositional analysis of Port Everglades Inlet microbiome using high throughput DNA sequencing

PeerJ
Lauren O'ConnellJose V Lopez

Abstract

Similar to natural rivers, manmade inlets connect inland runoff to the ocean. Port Everglades Inlet (PEI) is a busy cargo and cruise ship port in South Florida, which can act as a source of pollution to surrounding beaches and offshore coral reefs. Understanding the composition and fluctuations of bacterioplankton communities ("microbiomes") in major port inlets is important due to potential impacts on surrounding environments. We hypothesize seasonal microbial fluctuations, which were profiled by high throughput 16S rRNA amplicon sequencing and analysis. Surface water samples were collected every week for one year. A total of four samples per month, two from each sampling location, were used for statistical analysis creating a high sampling frequency and finer sampling scale than previous inlet microbiome studies. We observed significant differences in community alpha diversity between months and seasons. Analysis of composition of microbiomes (ANCOM) tests were run in QIIME 2 at genus level taxonomic classification to determine which genera were differentially abundant between seasons and months. Beta diversity results yielded significant differences in PEI community composition in regard to month, season, water temperature, ...Continue Reading

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Citations

Oct 1, 2019·PeerJ·Stephanie M RosalesLewis J Gramer

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Methods Mentioned

BETA
PCR
environmental stress
amplicon sequencing

Software Mentioned

PANDAseq
QIIME2
PERMANOVA
Quantitative Insights into Microbial Ecology 2 ( QIIME2 )
R package
phyloseq
DADA2
R
SAS
QIIME

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