ena-STUDY-INSTITUTE OF ENVIRONMENTAL BIOTECHNOLOGY, GRAZ UNI-29-08-2018-15:01:39:884-285
Arugula-associated Archaea
Sampling. Arugula plants were grown in garden soil (in the latter referred to bulk soil) in a suburban region of Graz (Austria). Edible plant parts consist of elongated leafs with short stalks and were termed as phyllosphere throughout this study when referring to the microbial habitat. The microbial fraction with Eruca sativa was extracted separately for the phyllo- and rhizosphere. In addition, a sample containing bluk soil was included. Samples from the abovementioned garden were obtained in early November at their final growth stage. The plants have already formed flowers and seed bodies. They were grown in a warm summer continental or hemiboreal climate, and the recorded climate profiles starting two weeks before sampling show relatively warm temperatures, moderate but fluctuating precipitation-, sunshine- and atmospheric- pressure levels, overall low wind levels and average air humidity. For each of the sample types, 5 equal specimens were obtained. All samples were stored on ice and immediately processed after arrival at a nearby laboratory. In order to homogenize the samples, 5 g of plant material or bulk soil per replicate was physically disrupted with a sterile pestle and mortar, re-suspended in 10 ml of 0.85% NaCl, transferred in two 2 ml Eppendorf tubes and subsequently centrifuged (16500 g, 20 min, 4 °C). The obtained pellet was used for isolation of the total-community DNA with FastDNA® SPIN Kit for Soil (MP Biomedicals, Solon, OH, USA) according to the manufacturer's instructions. All DNA extracts were stored at -80°C before further processing. Extracted community DNA from the habitats soil, rhizosphere and phyllosphere of arugula plants were subjected to PCR-based barcoding.All PCR reactions were conducted as triplicates, purified with the Wizard SV Gel and PCR cleanup system (Promega, Madison, WI), and pooled in equimolar concentrations prior to sequencing. The Sequencing was then conducted using an Illumina MiSeq Personal Sequencer (GATC Biotech AG, Konstanz, Germany).
Sampling. Arugula plants were grown in garden soil (in the latter referred to bulk soil) in a suburban region of Graz (Austria). Edible plant parts consist of elongated leafs with short stalks and were termed as phyllosphere throughout this study when referring to the microbial habitat. The microbial fraction with Eruca sativa was extracted separately for the phyllo- and rhizosphere. In addition, a sample containing bluk soil was included. Samples from the abovementioned garden were obtained in early November at their final growth stage. The plants have already formed flowers and seed bodies. They were grown in a warm summer continental or hemiboreal climate, and the recorded climate profiles starting two weeks before sampling show relatively warm temperatures, moderate but fluctuating precipitation-, sunshine- and atmospheric- pressure levels, overall low wind levels and average air humidity. For each of the sample types, 5 equal specimens were obtained. All samples were stored on ice and immediately processed after arrival at a nearby laboratory. In order to homogenize the samples, 5 g of plant material or bulk soil per replicate was physically disrupted with a sterile pestle and mortar, re-suspended in 10 ml of 0.85% NaCl, transferred in two 2 ml Eppendorf tubes and subsequently centrifuged (16500 g, 20 min, 4 °C). The obtained pellet was used for isolation of the total-community DNA with FastDNA® SPIN Kit for Soil (MP Biomedicals, Solon, OH, USA) according to the manufacturer's instructions. All DNA extracts were stored at -80°C before further processing. Extracted community DNA from the habitats soil, rhizosphere and phyllosphere of arugula plants were subjected to PCR-based barcoding.All PCR reactions were conducted as triplicates, purified with the Wizard SV Gel and PCR cleanup system (Promega, Madison, WI), and pooled in equimolar concentrations prior to sequencing. The Sequencing was then conducted using an Illumina MiSeq Personal Sequencer (GATC Biotech AG, Konstanz, Germany).