Microbial population dynamics along a terrestrial Antarctic moisture gradient

Kevin Lee1, Tancredi Caruso2, Stephen Archer1, Len Gillman1, Maggie Lau3, Craig Cary4, Charles lee5, Stephen Pointing6, Maxime Sweetlove7

1 Auckland University of Technology, Auckland, New Zealand; 2 Queen’s University Belfast, Belfast, United Kingdom; 3 Princeton University, Princeton, United States; 4 University of Waikato, Hamilton, New Zealand; 5 University of Waikato, Hamilton, United States; 6 National University of Singapore, Singapore, Singapore; 7 Royal Belgian Institute of Natural Sciences, Rue Vautier 29, 1000, Brussels

Corresponding author(s): Kevin LeeTancredi CarusoStephen ArcherLen GillmanMaggie LauCraig CaryCharles leeStephen Pointing, Maxime Sweetlove (msweetlove@naturalsciences.be)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource Citation

Lee K, Caruso T, Archer S, Gillman L, Lau M, Cary C, lee C, Pointing S (2019): Microbial population dynamics along a terrestrial Antarctic moisture gradient. v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=microbes_terrestrial_antarctic_moisture_gradient&v=1.2

Abstract

Amplicon sequencing dataset (Illumina MiSeq) of Bacteria (16S ssu rRNA gene) in soil samples from the McMurdo Dry Valleys (Antarctica) taken along a moisture gradient.

Keywords: Metadata

Project details

Project title: Microbial population dynamics along a terrestrial Antarctic moisture gradient
Personnel: Kevin Lee
Funding: The research was funded by a grant from the New Zealand Ministry of Business, Innovation & Employment (UOWX1401) and Yale-NUS College Start-Up Fund.

Data published through GBIF: https://ipt.biodiversity.aq/resource?r=microbes_terrestrial_antarctic_moisture_gradient

Taxonomic coverage

General taxonomic coverage description: Bacteria, based on amplicon sequencing of the 16S ssu rRNA marker gene (v3-v4region)
Taxonomic ranks
Domain: Bacteria
Common names: Bacteria

Spatial coverage

General spatial coverage: McMurdo Dry Valleys, Victoria lands, Antarctica
Coordinates: 77°39'36''S and 77°39'28.8''S Latitude; 163°6'18''E and 163°7'37.2''E Longitude 

Temporal coverage: 2015

Methods

Method step description: Samples were thawed on ice and three 0.5 g extractions were conducted using the CTAB method optimized for Antarctic oligotrophic environmental samples (Archer et al., 2015). DNA yield was measured in ng/g soil. Illumina MiSeq libraries were prepared as per manufacturer’s protocol (Metagenomic Sequencing Library Preparation Part # 15044223 Rev. B; Illumina, San Diego, CA, United States) as previously described (Lee et al., 2016). PCR targeting the V3–V4 regions of bacterial and archaeal 16S rRNA gene with the primer set: PCR1 forward (5′ TCGTCGGCAGCGTCAGATGT GTATAAGAGA CAGCCTACGG GNGGCWGCAG 3′ ) and PCR1 reverse (5′ GTCTCGTGGG CTCGGAGATG TGTATAAGAG ACAGGACTAC HVGGGTATCT AATCC 3′) was conducted using KAPA HiFi Hotstart Readymix (Kapa Biosystems, Wilmington, MA, United States) and the following thermocycles: (1) 95◦C for 3 min, (2) 25 cycles of 95◦C for 30 s, 55◦C for 30 s, ◦C for 30 s, 72◦C for 5 min, and (3) holding the samples at 4◦C. The amplicons were then indexed using Nextera XT index kit (Illumina). AMPure XP beads (Beckman-Coulter, Brea, CA, United States) was used to purified the amplicon. Sequencing was conducted with an Illumina MiSeq system (Illumina) with the 500 cycle V2chemistry at Auckland University of Technology, New Zealand. A 5% PhiX spike-in was used, as per manufacturer’s recommendation.
Study extent description: Sampling was conducted around the hyporheic zone of Spaulding Pond, Taylor Valley in the McMurdo Dry Valleys of Antarctica, during the austral summer of 2015. Four transects were defined in north-east (S77◦ 39.489′ , E163◦ 07.501′ ), south-east (S77◦ 39.513′ , E◦ 163 07.626′ ), south (S77◦ 39.589′ , E◦ 163 07.006′ ), and north-west (S77◦ 39.470′, E◦163 06.336′) facing hyporheic moisture gradients.
Sampling description: We adopted a zonal sampling approach where soils were retrieved that matched visible delineations along linear transects extending across the hyporheic zone from the water’s edge at each sampling station: Zone (1) Saturated soil adjacent to water’s edge; Zone (2) Wet soil as indicated by dark coloration; Zone (3) Ephemerally wet soil, dry but with evidence for previous water indicated by surface evaporites; Zone (4) Dry soil with no indication of recent moisture. Soils from each zone in each transect were recovered using aseptic technique and saturated with Lifeguard solution (Qiagen, Netherlands) (n = 16) with parallel sampling for geochemical and moisture analysis (n = 16). All samples were stored in darkness frozen at -20oC until processed.

Metadata language: English
Date of metadata creation: 2019-02-18
Hierarchy level: Dataset

References
Lee, K. C., Archer, S. D. J., Caruso, T., Gillman, L., Lau, M. C., Cary, S. C., ... & Pointing, S. B. (2018). Stochastic and deterministic effects of a moisture gradient on soil microbial communities in the McMurdo Dry Valleys of Antarctica. Frontiers in Microbiology, 9, 2619.