Isolation of Fungi from Lake Vostok Accretion Ice

Here we report the characterization of fungi from 10 accretion ice sections (3300-5100 y old) as well as two deep glacial ice sections that are close to the bottom of the glacier (1 000 000-2 000 000 y old) from the Vostok, Antarctica, 5G ice core. Fungi were characterized by fluorescence microscopy culturing and sequence analyses of ribosomal DNA internal transcribed spacers. A total of 270 fungal colonies were cultured from the accretion ice of subglacial Lake Vostok and an additional 14 from the glacial ice immediately above the accretion ice. Mean concentrations were 0-4.42 cells mL-1 ice meltwater of which 0-100% exhibited viability (as determined by fluorescence microscopy). Thirty-one unique fungal ribosomal DNA sequences (28 from accretion ice and three from glacial ice) were determined and compared to recent taxa. The results, plus tests for growth at low temperatures, indicated that Lake Vostok contains a mixture of heterotrophic psychrotolerant fungal species. This indicates that the lake is not sterile but contains a unique ecosystem

Subglacial Lake Vostok (Antarctica) Accretion Ice Contains a Diverse Set of Sequences from Aquatic, Marine and Sediment-Inhabiting Bacteria and Eukarya

Lake Vostok, the 7th largest (by volume) and 4th deepest lake on Earth, is covered by more than 3,700 m of ice, making it the largest subglacial lake known. The combination of cold, heat (from possible hydrothermal activity), pressure (from the overriding glacier), limited nutrients and complete darkness presents extreme challenges to life. Here, we report metagenomic/metatranscriptomic sequence analyses from four accretion ice sections from the Vostok 5G ice core. Two sections accreted in the vicinity of an embayment on the southwestern end of the lake, and the other two represented part of the southern main basin. We obtained 3,507 unique gene sequences from concentrates of 500 ml of 0.22 μm-filtered accretion ice meltwater. Taxonomic classifications (to genus and/or species) were possible for 1,623 of the sequences. Species determinations in combination with mRNA gene sequence results allowed deduction of the metabolic pathways represented in the accretion ice and, by extension, in the lake. Approximately 94% of the sequences were from Bacteria and 6% were from Eukarya. Only two sequences were from Archaea. In general, the taxa were similar to organisms previously described from lakes, brackish water, marine environments, soil, glaciers, ice, lake sediments, deep-sea sediments, deep-sea thermal vents, animals and plants. Sequences from aerobic, anaerobic, psychrophilic, thermophilic, halophilic, alkaliphilic, acidophilic, desiccation-resistant, autotrophic and heterotrophic organisms were present, including a number from multicellular eukaryotes. © 2013 Shtarkman et al

Instructional Models for Course-Based Research Experience (CRE) Teaching

The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert CRE instructors. Using a qualitative content analysis approach, the survey data were analyzed for the aims of inquiry instruction and pedagogical practices used to achieve these goals. The results characterize CRE inquiry teaching as involving three instructional models: 1) being a scientist and generating data; 2) teaching procedural knowledge; and 3) fostering project ownership. Each of these models is explicated and visualized in terms of the specific pedagogical practices and their relationships. The models present a complex picture of the ways in which CRE instruction is conducted on a daily basis and can inform instructors and institutions new to CRE teaching

Genomic diversity of bacteriophages infecting Microbacterium spp

The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, and their G+C% content ranges from 51.4% to 71.4%, compared to ~67% for their Microbacterium hosts. The phages were isolated on five different Microbacterium species, but typically do not efficiently infect strains beyond the one on which they were isolated. These Microbacterium phages contain many novel features, including very large viral genes (13.5 kbp) and unusual fusions of structural proteins, including a fusion of VIP2 toxin and a MuF-like protein into a single gene. These phages and their genetic components such as integration systems, recombineering tools, and phage-mediated delivery systems, will be useful resources for advancing Microbacterium genetics

Instructional Models for Course-Based Research Experience (CRE) Teaching

The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert CRE instructors. Using a qualitative content analysis approach, the survey data were analyzed for the aims of inquiry instruction and pedagogical practices used to achieve these goals. The results characterize CRE inquiry teaching as involving three instructional models: 1) being a scientist and generating data; 2) teaching procedural knowledge; and 3) fostering project ownership. Each of these models is explicated and visualized in terms of the specific pedagogical practices and their relationships. The models present a complex picture of the ways in which CRE instruction is conducted on a daily basis and can inform instructors and institutions new to CRE teaching

Isolation of Bacteria and Fungi from Lake Vostok Accretion Ice

Lake Vostok, located below the 4000 m thick Antarctic Ice Sheet, is the largest subglacial lake in Antarctica. The lake water has not been sampled due to concerns of forward contamination. However, ice cores available from the Vostok 5G well of depths greater than 3538 m represent lake water that has accreted to the overhead glacier from various regions across Lake Vostok. Here, we report the characterization of bacteria and fungi from ten accretion ice sections (15,000 to 18,000 years old), and two deep glacial ice sections (1 to 2 million years old) from the Vostok, Antarctica 5G ice core. Fungi, as well as bacteria, were characterized by fluorescence microscopy, scanning electron microscopy, culturing, and sequence analyses of ribosomal DNA. A total of 703 bacteria and fungi were cultured from the accretion ice of subglacial Lake Vostok. Mean cell concentrations were from 2.3 to 12.3 cells per ml of ice meltwater, of which 5 to 84% were viable. These cell counts are substantially lower than previously reported values. A total of 54 unique ribosomal DNA sequences were determined and compared to recent taxa, of which 36 were fungi and 18 were bacteria. Fungi most closely related to Rhodotorula, Aureobasidium, Cryptococcus, Cladosporium and Penicillium, and bacteria related to Carnobacterium spp., Bacillus spp., Caulobacter and Micrococcus were identified based on sequence analysis from cultured isolates. These findings, plus tests for growth at low temperatures, indicate that Lake Vostok contains a mixture of heterotrophic psychrotolerant and psychrophilic species. The results revealed new genera of microorganisms not previously reported in Lake Vostok accretion ice, lower abundances of microorganisms, and demonstrated the necessity to use multiple methods to thoroughly characterize environmental ice