Bacteria (16S) in growth laminae of a large conical mats from Lake Untersee, East Antarctic

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Koo H, Mojib N, Hakim J, Hawes I, Tanabe Y, Andersen D, Bej A (2019): Bacteria (16S) in growth laminae of a large conical mats from Lake Untersee, East Antarctic. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=bacteria_microbial_mats_lake_untersee_antarctica&v=1.1

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此資料的發布者及權利單位為 SCAR - Microbial Antarctic Resource System。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

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關鍵字

Metadata

聯絡資訊

地理涵蓋範圍

Lake Untersee, East Antarctica

分類群涵蓋範圍

Bacteria (16S ssu rRNA gene v3-v5)

Cyanobacteria (16S ssu rRNA gene, group specific primer)

時間涵蓋範圍

計畫資料

無相關描述

參與計畫的人員:

取樣方法

The core was collected by gently inserting a 50 mm diameter sterile polycarbonate core tube through the top of a conical mat structure, then sealing it with rubber stoppers and returning it to the surface. The core was stored in Antarctic Logistics Centre International (ALCI), Cape Town, South Africa facility first at -20°C in a walk-in freezer and then transported to UAB in dry ice and kept in -20°C freezer until used. The top three laminae (herein U1, top lamina; U2, middle lamina; and U3, inner lamina) were separated from the core and selected individually for sequencing. Each lamina was carefully separated using sterile forceps and rinsed with distilled water to avoid carryover of microorganisms between laminae before DNA extraction.

方法步驟描述:

1. Five samples from different segments of each lamina of the large conical mat were sliced with a sterile scalpel, transferred into separate microcentrifuge tubes consisting of beads (MO BIO Laboratories Inc., Carlsbad, CA, United States), and homogenized in a high velocity bead beater (BIO101/Savant FastPrep FP120 – Qiagen, Inc., Valencia, CA, United States). DNA was then purified using the PowerBiofilm®DNA isolation Kit (MO BIO Laboratories). The large conical mats used in this study are unique, found only in Lake Untersee. Therefore, to minimize sample collection while obtaining sufficient DNA to investigate the microbial composition of the mat laminae, we used five spatially representative samples from each lamina, and pooled the purified DNA into single samples for amplicon sequencing. The concentration and the quality of the pooled DNA from each mat lamina was determined by using a Lambda II spectrophotometer (Perkin Elmer, Norwalk, Conn.) followed by agarose gel electrophoresis (1% wt/vol agarose in 1X Tris-Acetate-EDTA (TAE) buffer, pH 7.8) to confirm that each sample consists of mostly high molecular weight DNA (>2 kbp). The DNA was then dried in a Savant Speedvac Evaporator SVC 100H and stored at 4°C until used for sequencing.
2. Bacterial tag-encoded amplicon pyrosequencing was performed using the primers 341F (5′–CCTACGGGAGGCAGCAG–3′) and 907R (5′–CCGTCAATTCMTTTGAGTTT–3′) targeting the V3–V5 region of the 16S rRNA, combined with group-specific primers for cyanobacterial: CYA106F (5′- CGGACGGGTGAGTAACGCGTGA-3′) and CYA781R (5′-GACTACWGGGGTATCTAATCCCWTT-3′). First, a sequencing library was established by using a one-step PCR method with a total of 30 cycles of template DNA amplification with the HotStarTaq Plus Master Mix kit (Qiagen, Inc., Valencia, CA, United States), and amplicons originating and extending from the aforementioned bacteria- and cyanobacteria-specific primers. Then, tag-encoded FLX amplicon pyrosequencing was performed on a Roche 454 FLX instrument with Titanium reagents following the Titanium procedures and RTL protocols at the Research and Testing Laboratory (Lubbock, TX, United States).

引用文獻

1. Koo, H., Mojib, N., Hakim, J. A., Hawes, I., Tanabe, Y., Andersen, D. T., & Bej, A. K. (2017). Microbial communities and their predicted metabolic functions in growth laminae of a unique large conical mat from Lake Untersee, East Antarctica. Frontiers in microbiology, 8, 1347.

額外的詮釋資料