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

Последняя версия опубликована SCAR - Microbial Antarctic Resource System Mar 19, 2019 SCAR - Microbial Antarctic Resource System

Amplicon sequencing dataset (454 pyrosequencing) of Bacterial communities (based on the 16S ssu rRNA gene; using Bacteria and Cyanobacteria-specific primers), of three different strata in a laminated microbial mat sample from Lake Untersee (east Antarctica)

Загрузки

Скачайте последнюю версию метаданных ресурса (только метаданные) в формате EML или RTF:

Метаданные в формате EML Скачать в English (12 KB)
Метаданные в формате RTF Скачать в English (13 KB)

Версии

В таблице ниже указаны только опубликованные версии ресурса, которые доступны для свободного скачивания.

Как оформить ссылку

Исследователи должны дать ссылку на эту работу следующим образом:

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

Права

Исследователи должны соблюдать следующие права:

Публикующей организацией и владельцем прав на данную работу является SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

Регистрация в GBIF

Этот ресурс был зарегистрирован в GBIF, ему был присвоен следующий UUID: 5ca9edf4-bb76-44d5-a962-bdef14a40c4f.  SCAR - Microbial Antarctic Resource System отвечает за публикацию этого ресурса, и зарегистрирован в GBIF как издатель данных при оподдержке Scientific Committee on Antarctic Research.

Ключевые слова

Metadata

Контакты

Кто является создателем ресурса:

Hyunmin Koo
University of Alabama at Birmingham Birmingham US
Nazia Mojib
University of Alabama at Birmingham Birmingham US
Joseph Hakim
University of Alabama at Birmingham Birmingham US
Ian Hawes
University of Canterbury Christchurch NZ
Yukiko Tanabe
National Institute of Polar Research Tachikawa JP
Dale Andersen
University of Alabama at Birmingham Birmingham US
Asim Bej
University of Alabama at Birmingham Birmingham US

Кто может ответить на вопросы о ресурсе:

Hyunmin Koo
University of Alabama at Birmingham Birmingham US

Кем заполнены метаданные:

Maxime Sweetlove
Research assistent
Royal Belgian Institute for Natural Sciences Rue Vautier 29 1000 Brussels BE

Кто еще связан с данным ресурсом:

User

Географический охват

Lake Untersee, East Antarctica

Ограничивающие координаты Юг Запад [-71.2, 13.45], Север Восток [-71.2, 13.45]

Таксономический охват

Bacteria (16S ssu rRNA gene v3-v5)

Domain  Bacteria (Bacteria)

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

Domain  Cyanobacteria (Cyanobacteria)

Временной охват

Дата начала 2001-01-01

Данные проекта

Описание отсутсвует

Название Bacteria (16S) in growth laminae of a large conical mats from Lake Untersee, East Antarctic
Финансирование The creation of this dataset was funded by the Tawani Foundation of Chicago (6803099), the Trottier Family Foundation, NASA’s Exobiology and Astrobiology Programs (NNX08AO19G), and the Arctic and Antarctic Research Institute/Russian Antarctic Expedition.

Исполнители проекта:

Hyunmin Koo

Методы сбора

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.

Охват исследования The samples were taken from a single core of a conical mat from Lake Untersee, which was collected by scientific divers utilizing SCUBA by accessing the lake ecosystem through a hole made on the ∼3.5 m surface ice.

Описание этапа методики:

  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).

Библиографические ссылки

  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.

Дополнительные метаданные

Альтернативные идентификаторы 5ca9edf4-bb76-44d5-a962-bdef14a40c4f
https://ipt.biodiversity.aq/resource?r=bacteria_microbial_mats_lake_untersee_antarctica