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Research-based courses are a powerful way to engage undergraduates in the scientific process while simultaneously teaching participants relevant laboratory, analysis, and scientific communication skills. In most programs, students conduct a simulated project which effectively improves student conceptions of scientific thinking but does not produce research-quality data. The course described here delivered an authentic research experience by assigning undergraduates an objective from an active grant-funded project. Participants contributed to research aimed at culturing biodegrading thermophiles from hot springs in Yellowstone National Park. Students participated in a backcountry field experience, collecting environmental samples of their choosing and determining appropriate culturing conditions. Following high-temperature incubations, 16S rRNA gene sequencing identified enriched microbial populations, with analytical and microscopy methods tracking degradation and growth. Importantly, several teams successfully cultivated thermophilic plastic-degrading consortia. Student learning was assessed using several methods, including grade distributions on assignments and statistical comparisons of pre- and posttests. A consistent and, in most cases, statistically significant increase was observed in the students’ posttest scores. The grade distribution on summative assessments also suggests that students achieved the desired learning outcomes. Student perceptions of their learning and experience gains were high, with participants reporting improvements in components emphasized in the research activities. Overall, the findings highlight how involving undergraduates in real-world research projects can enhance student interest and ownership of scientific research, along with contributing quality data that inform active studies.

NASA has made great strides in the past five years to develop a suite of instruments for the International Space Station in order to perform molecular biology in space. However, a key piece of equipment that has been lacking is an instrument that can extract nucleic acids from an array of complex human and environmental samples. The Omics in Space team has developed the μTitan (simulated micro(μ) gravity tested instrument for automated nucleic acid) system capable of automated, streamlined, nucleic acid extraction that is adapted for use under microgravity. The μTitan system was validated using a whole cell microbial reference (WCMR) standard comprised of a suspension of nine bacterial strains, titrated to concentrations that would challenge the performance of the instrument, as well as to determine the detection limits for isolating DNA. Quantitative assessment of system performance was measured by comparing instrument input challenge dose vs recovery by Qubit spectrofluorometry, qPCR, Bioanalyzer, and Next Generation Sequencing. Overall, results indicate that the μTitan system performs equal to or greater than a similar commercially available, earth-based, automated nucleic acid extraction device. The μTitan system was also tested in Yellowstone National Park (YNP) with the WCMR, to mimic a remote setting, with limited resources. The performance of the device at YNP was comparable to that in a laboratory setting. Such a portable, field-deployable, nucleic extraction system will be valuable for environmental microbiology, as well as in health care diagnostics.

The described diversity within the domain Archaea has recently expanded due to advances in sequencing technologies, but many habitats that likely harbor novel lineages of archaea remain understudied. Knowledge of archaea within natural and engineered hydrothermal systems, such as hot springs and engineered subsurface habitats, has been steadily increasing, but the majority of the work has focused on archaea living in acidic or circumneutral environments. The environmental pressures exerted by the combination of high temperatures and high pH likely select for divergent communities and distinct metabolic pathways from those observed in acidic or circumneutral systems. In this review, we examine what is currently known about the archaea found in thermoalkaline environments, focusing on the detection of novel lineages and knowledge of the ecology, metabolic pathways and functions of these populations and communities. We also discuss the potential of emerging multi–omics approaches, including proteomics and metabolomics, to enhance our understanding of archaea within extreme thermoalkaline systems.

Aims Development of biomineralization technologies has largely focused on microbially induced carbonate precipitation (MICP) via Sporosarcina pasteurii ureolysis; however, as an obligate aerobe, the general utility of this organism is limited. Here, facultative and anaerobic haloalkaliphiles capable of ureolysis were enriched, identified and then compared to S. pasteurii regarding biomineralization activities. Methods and results Anaerobic and facultative enrichments for haloalkaliphilic and ureolytic micro-organisms were established from sediment slurries collected at Soap Lake (WA). Optimal pH, temperature and salinity were determined for highly ureolytic enrichments, with dominant populations identified via a combination of high-throughput SSU rRNA gene sequencing, clone libraries and Sanger sequencing of isolates. The enrichment cultures consisted primarily of Sporosarcina- and Clostridium-like organisms. Ureolysis rates and direct cell counts in the enrichment cultures were comparable to the S. pasteurii (strain ATCC 11859) type strain. Conclusions Ureolysis rates from both facultatively and anaerobically enriched haloalkaliphiles were either not statistically significantly different to, or statistically significantly higher than, the S. pasteurii (strain ATCC 11859) rates. Work here concludes that extreme environments can harbour highly ureolytic active bacteria with potential advantages for large scale applications, such as environments devoid of oxygen. Significance and impact of the study The bacterial consortia and isolates obtained add to the possible suite of organisms available for MICP implementation, therefore potentially improving the economics and efficiency of commercial biomineralization.

U.S. National Science Foundation (MCB 0702212); Montana Agricultural Experiment Station (911310); U.S. National Science Foundation (MCB 0702177)

The Cyanidiales are unicellular red algae that are unique among phototrophs. They thrive in acidic, moderately high-temperature habitats typically associated with geothermally active regions, although much remains to be learned about their distribution and diversity within such extreme environments. We focused on Yellowstone National Park (YNP), using culture-dependent efforts in combination with a park-wide environmental polymerase chain reaction (PCR) survey to examine Cyanidiales diversity and distribution in aqueous (i.e. submerged), soil and endolithic environments. Phylogenetic reconstruction of Cyanidiales biodiversity demonstrated the presence of Cyanidioschyzon and Galdieria lineages exhibiting distinct habitat preferences. Cyanidioschyzon was the only phylotype detected in aqueous environments, but was also prominent in moist soil and endolithic habitats, environments where this genus was thought to be scarce. Galdieria was found in soil and endolithic samples, but absent in aqueous habitats. Interestingly, Cyanidium could not be found in the surveys, suggesting this genus may be absent or rare in YNP. Direct microscopic counts and viable counts from soil samples collected along a moisture gradient were positively correlated with moisture content, providing the first in situ evidence that gravimetric moisture is an important environmental parameter controlling distribution of these algae. Significance and Impact of the Study The Cyanidiales are an order of unicellular eukaryotic algae that thrive in acidic geothermal environments. In this study, we report several novel observations relative to Cyanidiales ecology in Yellowstone National Park, including the following: (i) the identification of two phylogenetic lineages of Cyanidiales: Cyanidioschyzon and Galdieria; (ii) the absence of Galdieria in aquatic environments; (iii) the absence of Cyanidium and Galdieria phlegrea in prime Cyanidiales habitats; (iv) the cohabitation of Cyanidioschyzon and Galdieria in nonaqueous environments; and (v) the first in situ evidence regarding the relationship between soil moisture and Cyanidiales habitat preference and viability

Ultraviolet and high-intensity visible radiation generate reactive intermediates that damage phototrophic microorganisms. In Yellowstone National Park, the thermoacidophilic alga Cyanidioschyzon exhibits an annual seasonal biomass fluctuation referred to as 'mat decline', where algal viability decreases as ultraviolet and visible irradiances increase during summer. We examined the role irradiance might play in mat decline using irradiance filters that uncouple ultraviolet and visible effects along with custom microarrays to study gene expression in situ. Of the 6507 genes, 88% showed no response to ultraviolet or visible, implying that at the biomolecular level, these algae inhabit a chemostat-like environment and is consistent with the near constant aqueous chemistry measured. The remaining genes exhibited expression changes linked to ultraviolet exposure, to increased visible radiation, or to the apparent combined effects of ultraviolet and visible. Expression of DNA repetitive elements was synchronized, being repressed by visible but also influenced by ultraviolet. At highest irradiance levels, these algae reduced transcription of genes encoding functions involved with DNA replication, photosynthesis and cell cycle progression but exhibited an uptick in activities related to repairing DNA damage. This corroborates known physiological responses to ultraviolet and visible radiation, and leads us to provisionally conclude that mat decline is linked to photoinhibition.