Microbiome of the soft coral Lobophytum pauciflorum

Investigation of microbial community of L. pauciflorum, the potential for a sex-specific microbiome and the effect of environmental stress on microbial community

    Data Record Details
    Data record related to this publication Microbiome of the soft coral Lobophytum pauciflorum
    Data Publication title Microbiome of the soft coral Lobophytum pauciflorum
  • Description

    Investigation of microbial community of L. pauciflorum, the potential for a sex-specific microbiome and the effect of environmental stress on microbial community

  • Other Descriptors
    • Descriptor

      Investigation of microbial community of Lobophytum pauciflorum testing for the potential for a sex-specific microbiome and the effect of environmental stress on microbial community. L. pauciflorum colonies were collected around Orpheus Island in August 2013 and October 2014. For the sex-specific microbiome analyses, 17 L. pauciflorum colonies were brought to Orpheus Island Research Station (OIRS) and sex was determined via histology and/or spawning during coral spawning November 2014. One lobe was immediately snap frozen for total DNA extraction and the second lobe transferred into HEPES buffered seawater with 4 % formaldehyde for fixation. For the temperature and CO2 stress experiments, fragments of 6 Lobophytum pauciflorum colonies were collected around Orpheus island, transported and cultured in a 1000L tank with flow through at the Marine Aquaculture Research Facility Unit at James Cook University, Townsville for further propagation. After one week of acclimation the fragments were cut into two pieces for the first time followed by a recovery period of 3 days. The fragments were halved again so that 4 small fragments in total of each colony were obtained which were transported back to OIRS and left to acclimate for 2 weeks prior to experimental manipulation. For the CO2 treatment, natural seawater in a 500 L sump tank was acidified with 100% CO2 to reach a pH of 7.9 using a pH computer (Aquamedic AT-Control, Germany) as described in Watson et al. (2012). To control for an effect due to the sump tank, a non acidified 500 L sump tank was used. Following acidification, seawater was heated with in line pond titanium heaters (Weinu, Taiwan) to 32°C in two 60 L header tanks that were supplied with seawater from of the sump tanks by a pond pump (Bianco, Australia). Each of the 60 L header tanks fed seven 3 L aquaria in which the coral fragments were placed randomly, one coral fragment per tank (Appendices Figure 4.7). The flow through into each experimental aquarium was adjusted to 250 mL/min to ensure maintenance of experimental conditions. Coral were kept at a 12/12 h day/night cycle with Sanyo lights (Sydney, Australia) connected to a timer clock. After transferring the coral fragments into the experimental aquaria, temperature was increased in the heated 60L from 27 °C to 32 °C over 48 h, pH was decreased over 6 h after the temperature had reached 32 °C. Temperature and pHNBS (model MW102, Milwaukee, USA) were measured at least 3 times a day and coral performance monitored. The experiment time started when stressors had reached their experimental level, of a pH of 7.9 and temperature 32 °C, respectively. Samples for total DNA extraction and caspase activity assays were taken 1 and 12 days after the start, snap frozen in liquid nitrogen and stored at – 80 °C until processing.

      Data files included in this dataset are as follows:

      • Caspase_Assay_2.zip (all raw data and analysed data for the caspase activity measurements)
      • LoboSex_OTUtable_SILVA_min15_known_noChloros.txt (count matrix focusing on the sex-specific microbiome)
      • LpSexAnno4.txt (summarises sample locations and sex of collected tissue samples for sex-specific microbiome analysis)
      • LpSex_rep_set.fna (representative sequences for the assigned Operational Taxonomic Units or OTUs)
      • Global_core_otus_51.txt (counts matrix for the core microbiome (51% representation) analysing the effect of environmental stressors simulating global change)
      • Global_OTUtable_SILVA_min10_noChloros.txt (count matrix focusing on the effect of global change parameters on the microbiome)
      • Global_OTUtable_SILVA_min10.txt )count matrix focusing on the effect of global change parameters on the microbiome, focusing on those OTUs that had at least 10 counts)
      • GlobalAnno4.txt (summarises allocation of collected tissue samples with experimental parameters and collected coral colony)
      • Global_rep_set.fna (representation of sequences for the assigned OTUs)
      • LpSexTop20_Core51_Sequences.fasta (sequence data of the 20 most abundant OTUs in the sex-specific biome)
      • GlobalTop20_Core51_Sequences.fasta (sequences of the 20 most abundant OTUs in the microbiome of soft coral samples exposed to environmental stressors representing global change)
      • Global_CCAs_colour_Arial_new.png (constraint component analyses focusing on bacterial communities according to experimental treatment or sampling origin)
      • Caspase_Activity_colour_small.png (capase activity per experimental conditions or per colony of origin)
      • LpGlobal_final.R (R code for statistical analysis of the microbiome under experimental stress as well as analysed data)
      • LpSexTop20_Core51_OTUs.txt (counts matrix for the 20 most abundant OTUs of core microbiome (51% representation) analysing for sex specific differences)
      • LpSex_final.R (R code for statistical analysis)
      • LpSex_core_otus_4.txt (counts matrix for the microbiome of samples analysed for sex specific differences)
      • LpSex_core_otus_51.txt (counts matrix for the microbiome (51% representation) analysed for sex specific differences)
      • Heatmaps Arial.ong (heatmaps representing the 20 most abundant OTUs with closest known bacteria)
      • Global_CCAs.png (correspondence component analysis for microbiome under environmental stressors)
    • Descriptor type Full
    • Descriptor

      This dataset contains 20 files in MS Excel (.xlsx), Prism (.pzfx), Text (.txt), FASTA (.fna and .faster) and Portable Network Graphics (.png) formats. Prism files can be viewed using the free Prism viewer, see http://graphpad.com/support/faqid/788/ for details.

    • Descriptor type Note
  • Data type dataset
  • Keywords
    • Lobophytum pauciflorum
    • Spirochaetes
    • microbiome
    • soft coral
    • ARC Centre of Excellence for Coral Reef Studies
  • Funding source
  • Research grant(s)/Scheme name(s)
  • Research themes
    Tropical Ecosystems, Conservation and Climate Change
    FoR Codes (*)
    • 060503 - Microbial Genetics
    • 060602 - Animal Physiology - Cell
    SEO Codes
    Specify spatial or temporal setting of the data
    Temporal (time) coverage
  • Start Date
  • End Date
  • Time Period
    Spatial (location) coverage
  • Locations
    • Orpheus Island National Park, Queensland, Australia
    Data Locations

    Type Location Notes
    Physical Location Secure data section of the Tropical Data Hub (TDH) archive - eResearch Centre, James Cook University, Townsville, Queensland, Australia
    Attachment core_otus_51.txt This file contains the counts matrix for the core microbiome (at 51% representation) focusing on the sex-specific microbiome
    The Data Manager is: Wiebke Wessels
    College or Centre
    Access conditions Conditional: Contact researchdata@jcu.edu.au to request access to this data.
  • Alternative access conditions
  • Data record size 64.2MB
  • Related publications
      Name Wessels, Wiebke, Sprungala, Susanne, Watson, Sue-Ann, Miller, David J., and Bourne, David G. (2017) The microbiome of the octocoral Lobophytum pauciflorum: minor differences between sexes and resilience to short-term stress. FEMS Microbiology Ecology, 93 (5). pp. 1-13.
    • URL http://dx.doi.org/10.1093/femsec/fix013
    • Notes
    • Name Wessels, Wiebke (2016) Molecular bases of soft coral reproduction. PhD thesis, James Cook University.
    • URL https://researchonline.jcu.edu.au/51476/
    • Notes Chapter 4 is a more detailed version of the publication submitted to FEMS
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    • Notes
  • Related metadata (including standards, codebooks, vocabularies, thesauri, ontologies)
  • Related data
      Name NCBI BioProject PRJNA350227: Lobophytum pauciflorum
    • URL http://www.ncbi.nlm.nih.gov/bioproject/350227
    • Notes This entry contains raw sequence data of the microbial community associated with the soft coral Lobophytum pauciflorum generated with Illumina MiSeq (16S rRNA gene amplicon)
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    • Notes
    Select or add a licence for the data
    The data will be licensed under CC BY-NC: Attribution-Noncommercial 3.0 AU
  • Other Licence
  • Statement of rights in data Once access to the data has been obtained via negotiation with the data manager, use of the dataset is governed by the CC-BY-NC AU licence.
  • Data owners
      Wiebke Wessels
    Citation Wessels, Wiebke (2016): Microbiome of the soft coral Lobophytum pauciflorum. James Cook University. https://doi.org/10.4225/28/5837bc6084d68