Comparative evaluation of the indigenous microbial diversity vs. drilling fluid contaminants in the NEEM Greenland ice core.
Demonstrating that the detected microbial diversity in nonaseptically drilled deep ice cores is truly indigenous is challenging because of potential contamination with exogenous microbial cells. The NEEM Greenland ice core project provided a first-time opportunity to determine the origin and extent of contamination throughout drilling. We performed multiple parallel cultivation and culture-independent analyses of five decontaminated ice core samples from different depths (100-2051 m), the drilling fluid and its components Estisol and Coasol, and the drilling chips collected during drilling. We created a collection of diverse bacterial and fungal isolates (84 from the drilling fluid and its components, 45 from decontaminated ice, and 66 from drilling chips). Their categorization as contaminants or intrinsic glacial ice microorganisms was based on several criteria, including phylogenetic analyses, genomic fingerprinting, phenotypic characteristics, and presence in drilling fluid, chips, and/or ice. Firmicutes and fungi comprised the dominant group of contaminants among isolates and cloned rRNA genes. Conversely, most Proteobacteria and Actinobacteria originating from the ice were identified as intrinsic. This study provides a database of potential contaminants useful for future studies of NEEM cores and can contribute toward developing standardized protocols for contamination detection and ensuring the authenticity of the microbial diversity in deep glacial ice.
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Vanya
V
Miteva
Caroline
C
Burlingame
Todd
T
Sowers
Jean
J
Brenchley
D039903:Actinobacteria / Q000235:genetics* / Q000302:isolation & purification; D001203:Ascomycota / Q000235:genetics* / Q000302:isolation & purification; D001487:Basidiomycota / Q000235:genetics* / Q000302:isolation & purification; D044822:Biodiversity; D059018:DNA Contamination; D004783:Environmental Microbiology; D005798:Genes, Bacterial; D005800:Genes, Fungal; D006116:Greenland; D007053:Ice; D046448:Ice Cover / Q000382:microbiology*; D008969:Molecular Sequence Data; D058889:Molecular Typing; D010802:Phylogeny; D020560:Proteobacteria / Q000235:genetics* / Q000302:isolation & purification; D012336:RNA, Ribosomal, 16S / Q000235:genetics
D007053:Ice; D012336:RNA, Ribosomal, 16S
deep ice core drilling; drilling fluid; microbial contamination