URLhttps://www.bco-dmo.org/dataset/654116
Download URLhttps://www.bco-dmo.org/dataset/654116/data/download
Media Typetext/tab-separated-values
CreatedAugust 15, 2016
ModifiedSeptember 30, 2016
StateFinal no updates expected
Brief DescriptionFungal iTAG analyses on Peru Margin sediment core samples

Acquisition Description

Peru Margin subsurface sediments were sampled on IODP leg 201 site 1229A (10°58.5721’ S 77°57.4590’W) in 150.5 m water depth. Core depth at 1229A was 187 mbsf.

DNA was extracted from either 2 or 20 grams of exterior and interior core sediment from frozen (stored at -80 degree C) Peru Margin samples collected at 6 mbsf (2H2) and 95 mbsf (11H5), respectively, using the PowerSoil DNA Isolation Kit (MoBio Laboratories, USA). Extractions were also performed for replicate samples collected from the exterior of both cores. The manufacturer’s protocol was modified to include five repetitions of homogenization for 1-minute intervals, with 1 minute rest in between, using a FastPrep benchtop homogenizer (MP Biomedicals, Santa Ana, CA) set to 4.0 m/s. A final purification step using isopropanol precipitation was also added. Duplicate extractions were performed for both interior and exterior regions of each core. Partial small-subunit ribosomal DNA (SSU rDNA) fragments were PCR amplified from DNA extracts using the key-tagged fungal-targeting primer set nu-SSU-0817-5’ and nu-SSU-1196-3’ (Borneman and Hartin, 2000). Replicate PCR amplifications (3-6) were run for each sample using Phusion High-Fidelity DNA Polymerase (ThermoFisher Scientific, USA) and 5X Phusion HF Buffer. PCR conditions were: 98 degrees C for 30 seconds followed by 40 cycles of 98 degrees C for 10 seconds, 56 degrees C for 30 seconds, and 72 degrees C for 30 seconds, and a final incubation for 7 minutes at 72 degrees C. PCR products were visualized by agarose gel electrophoresis and positive results were excised and purified from the gel using the ZymoClean Gel DNA recovery Kit (Zymo Research, USA). Purified replicate PCR amplifications from each sample were combined prior to iTAG sequencing using Illumina MiSeq PE300 at Georgia Genomics Center.

Processing Description

Raw read files were deposited in GenBankSRA under accession number SRP072127.

Instruments

The JOIDES Resolution's Advanced Piston Corer (APC) is used in soft ooze and sediments. The APC is a hydraulically actuated piston corer designed to recover relatively undisturbed samples from very soft to firm sediments.

More information is available from IODP (PDF).

General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

Instance Description

Purified replicate PCR amplifications from each sample were combined prior to iTAG sequencing using Illumina MiSeq PE300 at Georgia Genomics Center.

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Parameters

cruise_id [cruise_id]
Details
cruise_id
Cruise identifier
cruise designation; name
location [site]
Details
location
Sampling location
Sampling site identification.
lat [latitude]
Details
lat
Latitude of sampling location

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

lon [longitude]
Details
lon
Longitude of sampling location

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes

Details
core_depth

Depth of the sediment core

Meters below seafloor (mbsf); convention used for depths below the seabed in geology, oceanography, petrology and ocean drilling; often used in reporting measurements made from sediment cores.

sample_depth [meters below seafloor]
Details
sample_depth

Depth from which the samples were taken

Meters below seafloor (mbsf); convention used for depths below the seabed in geology, oceanography, petrology and ocean drilling; often used in reporting measurements made from sediment cores.

accession_num [accession number]
Details
accession_num
GenBank SRA accession number
Database identifier assigned by repository and linked to GenBank or other repository.
accession_link [accession number]
Details
accession_link
Hyperlink to GenBank SRA for the accession number
Database identifier assigned by repository and linked to GenBank or other repository.

Dataset Maintainers

NameAffiliationContact
Virginia P. EdgcombWoods Hole Oceanographic Institution (WHOI)
Maria G. PachiadakiWoods Hole Oceanographic Institution (WHOI)
Gaëtan BurgaudUniversite de Brest
Shannon RauchWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project TitleExploring of the Ecological Role(s) of Marine Fungi in the Deep Subseafloor
AcronymFungal and prokaryotic activity in subseafloor
URLhttps://www.bco-dmo.org/project/653744
CreatedAugust 10, 2016
ModifiedAugust 10, 2016
Project Description

The deep sedimentary biosphere, extending hundreds of meters below the seafloor harbors unexpected diversity of Bacteria, Archaea and microbial eukaryotes. Far less is known about microbial eukaryotes in subsurface habitats, albeit several studies have indicated that fungi dominate microbial eukaryotic communities and fungal molecular signatures (of both yeasts and filamentous forms) have been detected in samples as deep as 1740mbsf. Here we compare and contrast fungal ribosomal RNA gene signatures and whole community metatranscriptomes present in sediment core samples from 6 and 95mbsf from Peru Margin site 1229A and from samples from 12 and 345 mbsf from Canterbury Basin site U1352. The metatranscriptome analyses reveal higher relative expression of amino acid and peptide transporters in the less nutrient rich Canterbury Basin sediments compared to the nutrient rich Peru Margin, and higher expression of motility genes in the Peru Margin samples. Higher expression of genes associated with metals transporters and antibiotic resistance and production was detected in Canterbury Basin sediments. A poly-A focused metatranscriptome produced for the Canterbury Basin sample from 345 mbsf provides further evidence for active fungal communities in the subsurface in the form of fungal-associated transcripts for metabolic and cellular processes, cell and membrane functions, and catalytic activities. Fungal communities at comparable depths at the two geographically separated locations appear dominated by distinct taxa. Differences in taxonomic composition and expression of genes associated with particular metabolic activities may be a function of sediment organic content as well as oceanic province. Microscopic analysis of Canterbury Basin sediment samples from 4 and 403 mbsf produced visualizations of septate fungal filaments, branching fungi, conidiogenesis and spores. These images provide another important line of evidence supporting the occurrence and activity of fungi in the deep subseafloor biosphere.

This project was funded by C-DEBI sub-award #49538097.

Project Maintainers
NameAffiliationRoleContact
Virginia P. EdgcombWoods Hole Oceanographic Institution (WHOI)Principal Investigator
Maria G. PachiadakiWoods Hole Oceanographic Institution (WHOI)Co-Principal Investigator
Gaëtan BurgaudUniversite de BrestInternational Collaborator
Menu