Research Data

Coral metagenome: uncultured bacterium random survey

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General
Title
Coral metagenome: uncultured bacterium random survey
Type
Dataset
Date Record Created
2017-11-17
Date Record Modified
2018-01-05
Language
English
Coverage
Date Coverage
(no information)
Time Period
(no information)
Geospatial Location
Description
Descriptions
  1. Type: full

    Coral metagenome for study on changes in coral associated microbial populations associated with reef fish territories from the National Center for Biotechnology Information (NCBI) BioProject number PRJNA248936. Submitted by James Cook University, ARC Centre of Excellence  for Coral Reef Studies, ARC Grant ID CE0561435.

    Abstract [Related Publication]: Microbial community structure on coral reefs is strongly influenced by coral–algae interactions; however, the extent to which this influence is mediated by fishes is unknown. By excluding fleshy macroalgae, cultivating palatable filamentous algae and engaging in frequent aggression to protect resources, territorial damselfish (f. Pomacentridae), such as Stegastes, mediate macro-benthic dynamics on coral reefs and may significantly influence microbial communities. To elucidate how Stegastes apicalis and Stegastes nigricans may alter benthic microbial assemblages and coral health, we determined the benthic community composition (epilithic algal matrix and prokaryotes) and coral disease prevalence inside and outside of damselfish territories in the Great Barrier Reef, Australia. 16S rDNA sequencing revealed distinct bacterial communities associated with turf algae and a two to three times greater relative abundance of phylotypes with high sequence similarity to potential coral pathogens inside Stegastes's territories. These potentially pathogenic phylotypes (totalling 30.04% of the community) were found to have high sequence similarity to those amplified from black band disease (BBD) and disease affected corals worldwide. Disease surveys further revealed a significantly higher occurrence of BBD inside S. nigricans's territories. These findings demonstrate the first link between fish behaviour, reservoirs of potential coral disease pathogens and the prevalence of coral disease.

    Design [SRA Experiment]: To determine the impact of territorial damselfish on microbial communities, we examined the bacterial composition of the EAM inside and outside damselfish territories. In the field, ten 50 mL EAM samples were collected from control plots outside of Stegastes’ territories, inside S. apicalis’ territories and inside S. nigricans’ territories. For the collections from S. apicalis’ and S. nigricans’ territories, samples were taken across two damselfish colonies, and each sample came from a different damselfish territory. Samples were immediately snap-frozen in liquid nitrogen, stored at -80C [39] and transported to James Cook University (JCU) for processing and DNA extractions. Samples were homogenized under liquid nitrogen, DNA was isolated using a PowerPlant DNA Isolation Kit (MO BIO Laboratories, Carlsbad, CA, USA) following the manufacturer’s instructions and DNA quality was checked using a nanodrop. 27f and 519r univeral reverse primers and the V1-V3 region of the 16S gene were used for amplification with a single-step 30 cycle PCR using a HotStarTaq Plus Master Mix Kit (Qiagen, Valencia, CA, USA). MR DNA, a next generation sequencing and bioinformatics provider (Shallowater, TX, USA), performed the PCR (under the following conditions: 94C for 3 minutes, 28 cycles of 94C for 30 seconds, 53C for 40 seconds and 72C for 1 minute; 72C for 5 minutes). All amplicon products were mixed in equal concentrations and purified using Agencourt ampure beads (Agencourt Bioscience Corporation, MA, USA) and sequenced with Roche 454 FLX titanium instruments and reagents according to manufacturer’s guidelines.

Related Publications
  1. Casey, Jordan M., Ainsworth, Tracy D., Choat, J. Howard, and Connolly, Sean R. (2014) Farming behaviour of reef fishes increases the prevalence of coral disease associated microbes and black band disease. Proceedings of the Royal Society of London Series B, Biological Sciences, 281 (1788). pp. 1-8.
Related Websites
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Related Data
  1. Has part: >> SRZ573417: Epilithic associates
    • ID: https://www.ncbi.nlm.nih.gov/sra/SRX573417 (EXTERNAL)
    • Note(s): SRA Experiment
    • Publish to RDA: This related object (and relationship) is NOT being published to RDA.
  2. Has part: >> Microbe samples from coral metagenome
    • ID: https://www.ncbi.nlm.nih.gov/biosample?Db=biosample&DbFrom=bioproject&Cmd=Link&LinkName=bioproject_biosample&LinkReadableName=BioSample&ordinalpos=1&IdsFromResult=248936 (EXTERNAL)
    • Note(s): BioSamples (25)
    • Publish to RDA: This related object (and relationship) is NOT being published to RDA.
Related Services
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Technical metadata
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People
Creators
  1. Managed by: Ms Jordan Casey , jordan.casey1@jcu.edu.au , ARC Centre of Excellence for Coral Reef Studies
  2. Associated with: Dr Tracy Ainsworth , tracy.ainsworth@jcu.edu.au , ARC Centre of Excellence for Coral Reef Studies, Molecular and Cell Biology
  3. Associated with: Empro John Choat , john.choat@jcu.edu.au , Marine & Aquaculture Research Facilities, Marine Biology & Aquaculture
  4. Associated with: Prof Sean Connolly , sean.connolly@jcu.edu.au , ARC Centre of Excellence for Coral Reef Studies, Marine Biology & Aquaculture
Primary Contact
Ms Jordan Casey, jordan.casey1@jcu.edu.au
Supervisors
(no information)
Collaborators
(no information)
Subject
Fields of Research
  1. 060205 - Marine and Estuarine Ecology (incl. Marine Ichthyology) (060205)
Socio-Economic Objective
  1. 960808 - Marine Flora, Fauna and Biodiversity (960808)
Keywords
  1. microbial populations
  2. coral reefs
  3. epilithic algal matrix
  4. coral metagenome
  5. DNA sequences
  6. ARC Centre of Excellence for Coral Reef Studies
Research Activity
(no information)
Research Themes
Tropical Ecosystems, Conservation and Climate Change
Rights
License
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License - Other
(no information)
Access Rights/Conditions
NCBI places no restrictions on the use or distribution of data.
Type
open
Rights
(no information)
Data
Data Location
Online Locations
  1. https://www.ncbi.nlm.nih.gov/bioproject/248936
Stored At
(no information)
Citation
Cite:
Casey, J.; Ainsworth, T.; Choat, J.; Connolly, S. (2014). Coral metagenome: uncultured bacterium random survey. James Cook University. (dataset). e90bd17de0a434aa5b1160d55f2f1331