Microbial community composition of lake sediment in Thule, Greenland during the summer of 2014

• Main Author: Berdy, Brittany
• Format: Dataset
• Language: English
• Published: Arctic Data Center 2018
• Subjects: Arctic; Arctic Lake; Greenland; Thule
• Online Access: https://dx.doi.org/10.18739/a2930nv40; https://arcticdata.io/catalog/#view/doi:10.18739/A2930NV40

Microbes have survived, and thrived, on our planet for at least 3.5 billion years, and yet we know surprisingly little about these organisms, in large part due to the phenomenon of uncultivability. The phenomenon of uncultivability was first noted in 1898, and it has continuously been observed that the number of microbial cells in samples are inconsistent with the number of colonies formed on nutrient media, now known as “The Great Plate Count Anomoly.” To this day, much of what we know about microbes is from culture-independent approaches, and the majority of microbial species in nature remain uncultivated. It has been shown previously that growing microorganisms in their natural environment (in situ) can greatly increase recovery, likely due to the availability of critical growth factors present in their native habitat, but absent within the lab. Here, we compare standard cultivation approaches with a variety of in situ based cultivation techniques to grow microorganisms in an extreme environment of the High Arctic (lake sediment in Thule, Greenland). Cultivation experiments were performed on 3 occasions throughout the summer of 2014 using either standard cultivation, five in situ devices, or under anaerobic conditions. The resulting culture collections were compared. A total of 1173 isolates were cultivated and, utilizing PCR-aided amplification of the 16S rRNA gene, taxonomically identified using the Silva v.117 database. Our isolates grouped into 183 OTUs, across 89 generas and 24 Orders, representing 4 bacterial phyla, 1 eukaryotic phylum. We observed minimal overlap among culture collections obtained by different approaches: only 21 of 183 OTUs were common among all three techniques (standard, in situ, anaerobic), with both standard and in situ methods resulting in large, byt unique collections. Representatives from the orders Xanthomonadales, Streptomycetales, and Cytophagales were isolated exclusively by traditional cultivation, while isolates belonging to the orders Solirubrobacterales, Chromatiales, and Bacillales were cultivated exclusively by the in situ approaches. Overall, our results show that multiple methods of cultivation should be employed in conjunction to generate a thorough collection of isolates from a given environment.