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

Última versión Publicado por SCAR - Microbial Antarctic Resource System en 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)

Descargas

Descargue la última versión de los metadatos como EML o RTF:

Metadatos como un archivo EML descargar en Inglés (12 KB)
Metadatos como un archivo RTF descargar en Inglés (13 KB)

Versiones

La siguiente tabla muestra sólo las versiones publicadas del recurso que son de acceso público.

¿Cómo referenciar?

Los usuarios deben citar este trabajo de la siguiente manera:

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

Derechos

Los usuarios deben respetar los siguientes derechos de uso:

El publicador y propietario de los derechos de este trabajo es SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

Registro GBIF

Este recurso ha sido registrado en GBIF con el siguiente UUID: 5ca9edf4-bb76-44d5-a962-bdef14a40c4f.  SCAR - Microbial Antarctic Resource System publica este recurso, y está registrado en GBIF como un publicador de datos avalado por Scientific Committee on Antarctic Research.

Palabras Clave

Metadata

Contactos

¿Quién creó el recurso?:

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

¿Quién puede resolver dudas acerca del recurso?:

Hyunmin Koo
University of Alabama at Birmingham Birmingham US

¿Quién documentó los metadatos?:

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

¿Quién más está asociado con el recurso?:

Usuario

Cobertura Geográfica

Lake Untersee, East Antarctica

Coordenadas límite Latitud Mínima Longitud Mínima [-71.2, 13.45], Latitud Máxima Longitud Máxima [-71.2, 13.45]

Cobertura Taxonómica

Bacteria (16S ssu rRNA gene v3-v5)

Dominio  Bacteria (Bacteria)

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

Dominio  Cyanobacteria (Cyanobacteria)

Cobertura Temporal

Fecha Inicial 2001-01-01

Datos del Proyecto

No hay descripción disponible

Título Bacteria (16S) in growth laminae of a large conical mats from Lake Untersee, East Antarctic
Fuentes de Financiación 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.

Personas asociadas al proyecto:

Hyunmin Koo

Métodos de Muestreo

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.

Área de Estudio 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.

Descripción de la metodología paso a paso:

  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).

Referencias Bibliográficas

  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.

Metadatos Adicionales

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