Benthic microbial communities (Bacteria, 16S) of coastal terrestrial and ice shelf Antarctic meltwater ponds

Stephen Archer1, Ian McDonald1, Craig Herbold1, Charles Lee1, Craig Cary1, Maxime Sweetlove2

1 University of Waikato, Hamilton, New Zealand; 2 Royal Belgian Institute of Natural Sciences, Rue Vautier 29, 1000, Brussels

Corresponding author(s): Stephen ArcherIan McDonaldCraig HerboldCharles LeeCraig Cary, 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

Archer S, McDonald I, Herbold C, Lee C, Cary C (2019): Benthic microbial communities (Bacteria, 16S) of coastal terrestrial and ice shelf Antarctic meltwater ponds. v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=benthic_microbial_communities_16s_antarctic_meltwater_ponds&v=1.2

Abstract

The investigation of bacterioplankton, mat and sediment microbial communities from the Bratina Island meltwater ponds in Late November 2009, January 2012 and January 2013 and from meltwater ponds at the mouth of the Miers Valley in January 2013 using 16S rRNA pyrosequencing. Ponds range in size from 1 to several hundred square meters in surface area, 1-4m in depth and represent a broad variety of unique geochemistries. They are formed in the landscape depressions and are maintained from local ice and snow melt.

Keywords: Occurrence; Bacterioplankton; meltwater; ponds; Bratina Island; McMurdo; Ice Shelf; mat; sediment; community;  microbial, 16S, sequencing, Metadata

Project details

Project title: Bacterial Communities in the meltwater ponds of the McMurdo region, Antarctica
Personnel: Stephen Archer
Funding: Logistical and Science support provided by the Antarctica New Zealand Postgraduate Research scholarships:
2009 - New Zealand Post/Antarctica New Zealand Scholarship
2012/13 - Sir Robin Irvine/Antarctica New Zealand Scholarship
Additional support from the University of Waikato and the International Centre for Terrestrial Antarctic Research
Study area descriptions/descriptor: Study sites - meltwater ponds formed in landscape depressions. Bratina Island site: Located in the McMurdo sound, 30km from Ross Island at the tip of Brown peninsular. Ponds located adjacent to the Bratina Island research camp on the McMurdo Ice shelf. Up to 30cm of marine derived sediments cover the Ice Shelf, ponds typically thaw completely during the summer and freeze completely in the winter.
Design description: Samples collected from the pond surface, water columns, mats and sediments of a number of geochemically variable meltwater ponds to describe the microbial community and the influence of geochemical, temporal and spatial to community structure. The ponds are extremely geochemically heterogeneous providing a representative overview of the typical pond chemistries across a range of Antarctic ponds.

Data published through GBIF: https://ipt.biodiversity.aq/resource?r=benthic_microbial_communities_16s_antarctic_meltwater_ponds

Taxonomic coverage

General taxonomic coverage description: Bacteria 16S ssu rRNA gene
Taxonomic ranks
Domain: Bacteria
Common names: Bacteria

Spatial coverage

General spatial coverage: Antarctica: Pond P70E, Huey and Legin on Bratina Island, and ponds Finch, Canary and Morepork in Miers Valley
Coordinates: 78°7'44.4''S and 78°0'50.4''S Latitude; 164°11'27.6''E and 165°33'7.2''E Longitude 

Methods

Method step description: 
- . 	DNA was extracted from 0.5 g ± 0.1 g of individual sediment sections using a modified bead-beating method (Coyne et al., 2001). Briefly, sediment was added to 0.5 g each of 0.1 mm and 2.5 mm silica-zirconia beads. To each sample 270 μL of phosphate buffer (100 mM NaH2PO4) and 270 μL of SDS lysis buffer (100 mM NaCl, 500 mM Tris pH 8.0, 10% SDS) were added and samples were horizontally shaken on a Vortex Genie 2 (MO BIO Laboratories Inc, Carlsbad, CA, USA) for 15 min. Samples were centrifuged at 12,500 rpm for 30 s and 180 μL of cetyltrimethylammonium bromide-polyvinylpyrrolidone (CTAB) extraction buffer (100 mM Tis-HCl, 1.4 M NaCl, 20 mM EDTA, 2% CTAB, 1% polyvinylpyrrlidone and 0.4% β-mecaptoethanol) was added. Samples were vortexed for 10 s prior to incubation at 60°C and 300 rpm for 30 min on a rocking bed. Samples were centrifuged at 12,500 rpm for 30 s and then 350 μL of chloroform/isoamyl alcohol (24:1) was added. Samples were again vortexed for 10 s and centrifuged for 5 min at 12,500 rpm. The aqueous phase was transferred to a new eppendorf tube then 500 μL of chloroform/isoamyl alcohol (24:1) was added. Samples were vortexed and left on a rocking bed HulaMixer (Invitrogen, Carlsbad, CA, USA) for 20 min. Samples were centrifuged for 5 min at 13,500 rpm, the aqueous phase was removed and 10 M ammonium acetate was added to the samples to achieve a final concentration of 2.5 M. The samples were vortexed and centrifuged for 5 min at 13,500 rpm. The aqueous layer was removed to a new tube and 0.54 volumes of isopropanol was added and mixed. Samples were left overnight at −20°C then centrifuged for 20 min at 13,500 rpm. The supernatant was removed, the pellet washed with 1 mL of 70% AR grade ethanol and centrifuged for 1 min at 13,500 rpm. Ethanol was removed and DNA was re-suspended in 30 μL of sterile TE then quantified using the Qubit 2.0 Florometer (Invitrogen). The four individual sectioned samples from each core were diluted to 10 ng/μL, then 10 μL of each was pooled and frozen at −20°C until use.
- . 	The V5-V6 hypervariable region of the 16S rRNA gene was utilized to identify variation in bacterial community diversity and structure. 30 μL PCR reactions were run in triplicate for each sample using un-adapted primers Tx9F (5′-GGATTAGAWACCCBGGTAGTC-3′) and 1391R (5′-GACGGGCRGTGWGTRCA-3′). The triplicates were pooled then gel extracted on a 2% TAE agarose gel stained with “SYBR Safe” and DNA was retrieved using the UltraClean 15 (MoBio, Inc, Carlsbad, USA) DNA Purification Kit as per manufacturers instructions. A second round of triplicate PCR was run as above but with only 10 cycles and using 25 ng of the purified DNA from the previous step per reaction (milli-Q H2O volume adjusted accordingly). The primers used were adapted for one-way reads as per manufacturers instructions, including unique MID identifiers for each sample [BacX-Tx9F (5′-CCATCTCATCCCTGCGTGTCTCCGACTCAG-MID-GGATTAGAWACCCBGGTAGTC-3′) and BacB-1391R (5′-CCTATCCCCTGTGTGCCTTGGCAGTCTCAG-GACGGGCRGTGWGTRCA-3′)]. A second gel extraction was performed as above. Samples went through a final cleanup step using the Agencourt AMPure XP system (Beckman Coulter Genomics, Danvers, MA, USA) as per the manufacturers instructions.
- . 	The diluted amplicons were mixed together in the desired proportions to create the 1 × 109 amplicon pool. Sequencing was performed using the GS Junior Titanium emPCR Kit (Lib-L), the GS Junior Titanium Sequencing Kit, PicoTiterPlate Kit and GS Junior System according to the manufacturers instructions (Roche 454 Life Sciences, Branford, CT, USA).
Study extent description: Sampling area; Bratina Island ponds located within 1km from the study camp on the McMurdo Ice Shelf. Miers Valley ponds within 1km of the eastern mouth of the valley
Temporal - Samples were collected during the Austral summer in November 2009, January 2012 and January 2013, a single time point per pond per year
Sampling description: Samples were aseptically collected using a disposable push-corer developed from a 50 mL syringe (BD, Singapore). The corer (with the plunger removed) was inserted 4–6 cm into the sediment, the plunger reinserted and core removed carefully to retain the sediment structure. After excess sediment was removed, each core was sub-sectioned into four one-centimeter samples, placed in sterile 15 oz whirlpack (Nasco, WI, USA), then frozen for transportation to the laboratory.
Quality control description: Sample DNA content was quantified using a Qubit Fluorometer and diluted to 200 pg/μL. The DNA concentration and quality verification was performed using a 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) and then diluted to 1 × 109 molecules/μL.

Metadata language: English
Date of metadata creation: 2019-01-17
Hierarchy level: Dataset

References
Archer, S. D., McDonald, I. R., Herbold, C. W., Lee, C. K., & Cary, C. S. (2015). Benthic microbial communities of coastal terrestrial and ice shelf Antarctic meltwater ponds. Frontiers in microbiology, 6, 485.