Antarctic Surface Snow Bacterial Communities

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¿Cómo referenciar?

Los usuarios deben citar este trabajo de la siguiente manera:

Malard L, Sabacka M, Magiopoulos I, Mowlem M, Hodson A, Tranter M, Siegert M, Pearce D (2019): Antarctic Surface Snow Bacterial Communities. v1.0. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=antarctic_surface_snow_bacterial_communities&v=1.0

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. Esta obra está bajo una licencia Creative Commons de Atribución/Reconocimiento (CC-BY 4.0).

Registro GBIF

Este recurso ha sido registrado en GBIF con el siguiente UUID: f9644d4b-3c39-4147-9d84-4baff93e1737.  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.

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Metadata

Contactos

Cobertura geográfica

The region between the South Orkney Islands and the Ellsworth Mountains (Antarctica)

Cobertura taxonómica

Bacteria were profiled by targeting the v3-v4 region of the 16S ssu rRNA gene with the primers 341F and 785R

Datos del proyecto

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Personas asociadas al proyecto:

Métodos de muestreo

Snow was collected from the surface to represent collection during melt water production for hot-water drilling. At each sampling location, a 1 m snow pit was excavated and the top 30 cm of snow was sampled using an ethanol sterilized shovel and Whirl-Pak bags (Nasco, WI, United States). Samples were transported to the field laboratory, where they were melted and passed through 0.2 μm Sterivex filters (Merck, Darmstadt, Germany), before freezing at −20°C for transport and processing in the United Kingdom.

Descripción de la metodología paso a paso:

1. SkyBlu, Pine Island Bay and Ellsworth snow samples were processed in two ways; PMA-treated and non-PMA-treated in order to differentiate the potentially viable microbial community from relic DNA. Each 0.2 μm filter was cut in half using sterile and DNAase/ethanol treated razors. For each sample, one-half was processed with PMA as per Nocker and Camper (2009) and Fittipaldi et al. (2012), using a 20 mM stock solution of PMA (Biotium, Hayward, CA, United States) in a 20% (v/v) aqueous solution of dimethyl sulfoxide (DMSO). Filters for PMA treatment were placed in a 6-well plate and a PMA solution at a final concentration of 100 μM was added. Cross-linking was initiated by 10 min incubation on ice, in the dark with occasional mixing, followed by 5 min of light exposure using a 650 W halogen lamp (FLASH 2000 L, DTS, Italy), at a 20 cm distance. The process was carried out in a laminar flow hood to avoid contamination of the samples. Non-PMA-treated samples were incubated in a 20% (v/v) aqueous solution of DMSO, and treated following the same protocol as PMA-treated samples. All samples were washed twice with sterile phosphate buffered saline (PBS) and all samples were then used for DNA extraction. DNA from snow samples was extracted using the PowerWater kit from MoBio (Qiagen, Carlsbad, CA, United States). Each sample was PCR amplified using the primers 341F and 785R covering the V3-V4 regions of the 16S rRNA gene (Klindworth et al., 2013), under the following conditions: initial denaturation at 95°C for 5 min then 25 cycles of 40 s denaturation at 95°C; primer annealing at 55°C for 2 min; and elongation at 72°C for 1 min then a final elongation at 72°C for 7 min (Hodson et al., 2017). DNA extraction kit controls were included alongside the snow derived DNA and sequenced. PCR amplicons were cleaned, normalized, quantified and supplemented with 5% PhiX before being loaded on Illumina MiSeq, as per the Illumina standard operating protocol (Kozich et al., 2013).
2. DNA from snow samples was extracted using the PowerWater kit from MoBio (Qiagen, Carlsbad, CA, United States). Each sample was PCR amplified using the primers 341F and 785R covering the V3-V4 regions of the 16S rRNA gene, under the following conditions: initial denaturation at 95°C for 5 min then 25 cycles of 40 s denaturation at 95°C; primer annealing at 55°C for 2 min; and elongation at 72°C for 1 min then a final elongation at 72°C for 7 min (Hodson et al., 2017). DNA extraction kit controls were included alongside the snow derived DNA and sequenced. PCR amplicons were cleaned, normalized, quantified and supplemented with 5% PhiX before being loaded on Illumina MiSeq, as per the Illumina standard operating protocol (Kozich et al., 2013).

Referencias bibliográficas

1. Malard, L. A., Šabacká, M., Magiopoulos, I., Hodson, A., Tranter, M., Siegert, M. J., & Pearce, D. A. (2019). Spatial variability of Antarctic surface snow bacterial communities. Frontiers in Microbiology, 10, 461. https://doi.org/10.3389/fmicb.2019.00461

Metadatos adicionales