16S rRNA sequence analysis of silver carp microbial community in eDNA water samples

Ladell, Bridget Anne

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https://hdl.handle.net/2142/101368 Copy

Description

Title

16S rRNA sequence analysis of silver carp microbial community in eDNA water samples

Author(s)

Ladell, Bridget Anne

Issue Date

2018-04-23

Director of Research (if dissertation) or Advisor (if thesis)

Liu, Wen Tso

Department of Study

Civil & Environmental Eng

Discipline

Environ Engr in Civil Engr

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

M.S.

Degree Level

Thesis

Keyword(s)

eDNA, Microbial Community Analysis, Silver Carp, 16S, Invasive Species, Fusobacteria

Abstract

A 14-day study was conducted in a closed system taking triplicate environmental DNA (eDNA) water samples from 150 L tanks containing set numbers of invasive Silver Carp. Analysis eDNA samples typically involves only targeting the species of interest. However, eDNA detection alone cannot undeniably confirm the presence of the species of interest and a second line of evidence would be beneficial in making this assay more robust. A specific gut microbe within the phylum Fusobacteria has been identified as unique to fish species and Silver Carp specifically. The ability to detect these species alongside the Silver Carp DNA would establish two lines of evidence to determine the presence of a live fish in an area of interest. A better understanding of the composition of microbial biome in the gut as it is represented in the natural environment and a tool to track its presence was needed to effectively complete this work as well as an understand of how Silver Carp biomass affects these results. The study was scheduled over the course of several days and different numbers of Silver Carp present to elucidate the impact of time on the microbe of interest. For this, DNA was extracted and analyzed through 16S rRNA sequencing on the Illumina MiSeq platform yielding 25 million reads and over 16,000 OTUs after initial clean up. Following analysis, there were multiple microbial groups, in particular 127 OTUs within the Fusobacteria phylum previously determined to be specialized to the gut of Silver Carp that were present in eDNA samples throughout the length of study and this was most significantly present in study tanks with the greatest amount of Silver Carp. This work confirms the potential of implementing a second target for eDNA sampling of Silver Carp through the assistance of the gut microbiome composition.

Graduation Semester

2018-05

Type of Resource

text

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http://hdl.handle.net/2142/101368

Copyright and License Information

Copyright 2018 Bridget Ladell

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