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.

Evaluation of a new fluorimetric DNA-DNA hybridization method.

Standardized procedures must be followed when characterizing, officially describing, and validly naming novel bacteria. For species descriptions, DNA-DNA hybridization still is needed for whole-genome comparisons between close relatives, but many established hybridization methods have drawbacks, such as requiring labeled or large amounts of DNA. We evaluated a new technique based on the spectrophotometric method in which renaturation rates are used for calculating the degree of binding, which estimates relatedness.

Diversity and ecology of psychrophilic microorganisms.

Cold environments represent the majority of the biosphere on Earth and have been successfully colonized by psychrophilic microorganisms that are able to thrive at low temperatures and to survive and even maintain metabolic activity at subzero temperatures. These microorganisms play key ecological roles in their habitats and include a wide diversity of representatives of all three domains (Bacteria, Archaea, Eukarya). In this review, we summarize recent knowledge on the abundance, on the taxonomic and functional biodiversity, on low temperature adaptation and on the biogeography of microbial communities in a range of aquatic and terrestrial cold environments.

Novel ultramicrobacterial isolates from a deep Greenland ice core represent a proposed new species, Chryseobacterium greenlandense sp. nov.

Three novel orange, ultramicrobacterial isolates, UMB10, UMB14, and UMB34(T) were isolated from enrichment cultures inoculated with a melted 3,043 m deep Greenland ice core sample. Phylogenetic analysis of the 16S rRNA gene sequences indicated that the isolates belonged to a single species within the genus Chryseobacterium. They were most closely related to Chryseobacterium aquaticum (99.

Herminiimonas glaciei sp. nov., a novel ultramicrobacterium from 3042 m deep Greenland glacial ice.

A Gram-negative ultramicrobacterium (designated strain UMB49(T)) was isolated from a 120,000-year-old, 3,042 m deep Greenland glacier ice core using a 0.2 mum filtration enrichment procedure. Phylogenetic analysis of the 16S rRNA gene sequence indicated that this strain belonged to the genus Herminiimonas of the family Oxalobacteraceae of the class Betaproteobacteria.

Comparison of the microbial diversity at different depths of the GISP2 Greenland ice core in relationship to deposition climates.

This study presents comparative geochemical, microbiological and molecular analyses of Greenland GISP2 ice core samples representing different depths, ages, deposition climates, in situ temperatures, and gas and ionic compositions. Our goal was to determine whether specific organisms, preserved at different depths, correlate with past climate characteristics recorded chronologically in ice layers. Three clear ice samples were selected from 2495, 2545 and 2578 m to represent distinct climatic periods with milder (-45 degrees C), colder (-51 degrees C) and warmer (-39 degrees C) deposition temperatures, and two Marine Isotope Stages, MIS3 (2495 m) and MIS4 (2545 and 2578 m).

Characterization of a cryptic plasmid from a Greenland ice core Arthrobacter isolate and construction of a shuttle vector that replicates in psychrophilic high G+C Gram-positive recipients.

Over 60 Greenland glacial isolates were screened for plasmids and antibiotic resistance/sensitivity as the first step in establishing a genetic system. Sequence analysis of a small, cryptic, 1,950 bp plasmid, p54, from isolate GIC54, related to Arthrobacter agilis, showed a region similar to that found in theta replicating Rhodococcus plasmids. A 6,002 bp shuttle vector, pSVJ21, was constructed by ligating p54 and pUC18 and inserting a chloramphenicol acetyl transferase (CAT) cassette conferring chloramphenicol resistance.

Detection and isolation of ultrasmall microorganisms from a 120,000-year-old Greenland glacier ice core.

The abundant microbial population in a 3,043-m-deep Greenland glacier ice core was dominated by ultrasmall cells (<0.1 microm3) that may represent intrinsically small organisms or starved, minute forms of normal-sized microbes. In order to examine their diversity and obtain isolates, we enriched for ultrasmall psychrophiles by filtering melted ice through filters with different pore sizes, inoculating anaerobic low-nutrient liquid media, and performing successive rounds of filtrations and recultivations at 5 degrees C.

Structural and functional analysis of pt38, a 2.9kb plasmid of Streptococcus thermophilus yogurt strain.

The cryptic plasmid pt38 (2911 bp) of Streptococcus thermophilus ST2783, a strain isolated from Bulgarian yogurt, was subcloned and sequenced. Five ORFs (ORF1 to ORF5) were identified, although putative transcription initiation and termination signals, and Shine-Dalgarno sequence could only be localized for three of them (ORF1, ORF2, and ORF5). ORF2 would specify a 142-amino acid protein sharing a high degree of homology with plasmid-born low-molecular-weight heat stress proteins described in a variety of S.

Rhodoglobus vestalii gen. nov., sp. nov., a novel psychrophilic organism isolated from an Antarctic Dry Valley lake.

A novel, psychrophilic, gram-positive bacterium (designated strain LV3T) from a lake near the McMurdo Ice Shelf, Antarctica, has been isolated and characterized. This organism formed red-pigmented colonies, had an optimal growth temperature of 18 degrees C and grew on a variety of media between -2 and 21 degrees C. Scanning electron micrographs of strain LV3T that showed small rods with unusual bulbous protuberances during all phases of growth were of particular interest.

Phylogenetic analysis of anaerobic psychrophilic enrichment cultures obtained from a greenland glacier ice core.

The examination of microorganisms in glacial ice cores allows the phylogenetic relationships of organisms frozen for thousands of years to be compared with those of current isolates. We developed a method for aseptically sampling a sediment-containing portion of a Greenland ice core that had remained at -9 degrees C for over 100,000 years. Epifluorescence microscopy and flow cytometry results showed that the ice sample contained over 6 x 10(7) cells/ml.