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Grants List


Courtesy of MATBI, PaulReichert

Yellowstone Park Foundation

Model study to correlate metagenomics with environmental conditions in Yellowstone Lake

This project studied Yellowstone Lake microbial phylogenetic and functional gene diversity to assess if, and to what extent, their distribution patterns correlate with environmental parameters through comparative analyses with chemical and geological data of distinct sites in the lake. By combining genomic tools with detailed environmental niche characterization, the multidisciplinary team tested hypotheses about environmental selective pressures and their influences on functional gene diversity in aquatic ecosystems.

Title: Model study to correlate metagenomics with environmental conditions in Yellowstone Lake
Date Awarded: Sep 2007
Amount: $1,096,997
Term: 24 months
Grant ID: GBMF1555
Funding Area: Science, Marine Microbiology Initiative
Organization Name: Yellowstone Park Foundation


Yellowstone National Park has been fiercely guarded since the park’s inception (ca. 1872), and its streams and lakes are near pristine. Yellowstone Lake is the largest (~352 km2) sub-alpine high-altitude lake in North America. It is a non-regulated body of water with a maximum measured depth of 131 m, an average depth of ~43 m, and its 140 tributaries derive primarily from snowmelt. The lake’s food web is critical to the function of the Yellowstone ecosystem, with the wellbeing of some of the park’s charismatic megafauna (e.g., grizzly bear, otter, bald eagle) now recognized as being linked to the lake’s productivity via the Yellowstone cutthroat trout, a keystone species. Presumably, microbial food webs are foundational in this regard, yet surprisingly little is known about this or other aspects of the lake’s biology and how the lake accomplishes its important role.

In addition to the visually obvious vents and hot springs in Yellowstone that are world renowned, there are other inconspicuous hydrothermal vents on the floor of Yellowstone Lake. These vents are logistically simpler to access and study than the deep-sea vents and have distinct emissions that include energy-rich compounds such as H2 that provide opportunities for examining relationships between environmental features and microbial community composition and functional gene abundance.

Collectively, the team of scientists involved has been working on this lake for nearly a half century on different projects. For this particular effort, the focus was to examine whether the varying chemistry of the lake floor vents in the two geothermal active regions of the lake could be correlated with specific microorganisms and their functional genes. To attack this question, the team sampled the lake floor vent fluids and associated microbial streamers as well as the water directly above the vent where vent fluids mixed with the cold lake water (mixing zone). Additionally, lake surface waters, either directly above the vent or in regions of the lake where there were no known vents, were also sampled. The workhorse in this sampling effort involved a remotely operated vehicle (ROV) that was equipped with a video camera that allowed the ROV operator to locate vents, accurately position the ROV sampling device over the vent orifice, and then acquire vent emissions or mixing zone samples.

Microbial biomass in these samples was size-fractionated and DNA extracted and sequenced using high throughput pyrosequencing targeting the 16S and 18S rRNA genes as well as random total DNA fragments for metagenomic sequencing. The microbial diversity in these samples was estimated from sequences of roughly 1200 near full-length 16S rRNA genes and a combined ~1 million 454-FLX and 454-Titanium reads. In addition, metagenomic pyrosequence totaled > 6 billion bp for all vent, mixing zone, and photic zone samples acquired from across the lake.

One hypothesis the team tested was that the vent output would initiate a chemical/energy gradient within the overlying water column that would diminish with distance to the lake surface, but that would influence the composition of the microbial community and their various functional genes. As a contrast, lake surface waters not associated with vents were also sampled. 

For high volume vents in relatively shallow water (< 30 m), gas chemistries (CO2, H2, H2S, CH4) did indeed form gradients, with concentrations near the lake surface nearing background lake levels. The team found that vent output characteristics (pH, gases, solutes) influenced the type and abundance of the thermophiles observed in the vent emissions and streamers associated with the specific vent. Phylogenetic analysis of the vent organisms revealed close matches with thermophiles from other high temperature environments, including organisms forming clades with deep-sea vent organisms. Similar work with non-vent microbes also yielded interesting analogies with the marine environment. Specific examples include: i) near full length Sanger sequenced 16S rRNA gene PCR clones exhibiting a 100% match with the dominant marine phototroph Prochlorococcus; ii) 96% 16S rRNA match to the marine Thaumarchaeota ammonia oxidizer Nitrosopumilus; and iii) 96% match to the 18S rRNA of the sub-micron green alga Ostreococcus

The team identified some relationships between specific functional genes and relevant substrates. As one prominent example, even though H2 was found above microbial metabolic thresholds throughout the lake, this high-energy substrate was viewed as a marker for high output vents studied in the Inflated Plain area. The 10 m photic zone water overlying such vents could contain >20-fold more H2 than non-vent associated photic zone samples (e.g. Southeast Arm region), whereas the occurrence of H2 oxidation relevant genes (e.g. coenzyme F420 hydrogenase) was essentially present or absent at the depth of metagenomic sequence employed. Uncovering these function-substrate relationships required manual analysis of the 34 individual annotated metagenome libraries (~350,000–1,200,000 reads). Lake mixing/currents appear to have a large influence regarding horizontal distribution of taxa and functional genes.

A variety of Yellowstone Lake projects continue, both by the PIs as well as international groups utilizing the metagenome sequence generated from this project and that is publically available at the iMicrobe Data Commons.

From Marine Microbiology Initiative grantee Tim McDermott of Montana State University: Low-temperature hydrothermal vent in the West Thumb region of Yellowstone Lake. The vent is at a depth of 28 m and surrounded by a dense colony of the moss Fontinalis. The remote operating vehicle sampling arm is shown extended into the vent opening. Water temperature was ~35°C and the cloudy material being emitted from the vent was determined by SEM electron dispersive X-ray analysis to be an alumino-silicate. For further details, see: Lovalvo et al. 2010. A geothermal-linked biological oasis in Yellowstone Lake, Yellowstone National Park, Wyoming. Geobiology 8: 327–336.

From Marine Microbiology Initiative grantee Tim McDermott of Montana State University: High-temperature vent cluster located in the Inflated Plain (northern) region of Yellowstone Lake (94°C; depth, 31 m). Arrows illustrate orifices of two adjacent vents. Bubbles are comprised of hydrogen, carbon dioxide, methane and sulfide. Real-time temperature is shown in the lower right, with increasing temperature reflecting more precise positioning of the remote operated vehicle sampling arm over the orifice of a vent that was subsequently sampled for geochemical and microbial diversity analysis. For further details, see: Clingenpeel et al. 2011. Yellowstone Lake: high energy geochemistry and rich bacterial diversity. Environmental Microbiology 13: 2172–2185.


Read more:

1. Lovalvo, D., S. R. Clingenpeel, S. McGinnis, R. E. Macur, J. D. Varley, W. P. Inskeep, J. Glime, K. Nealson, and T. R. McDermott. 2010. A geothermal-linked biological oasis in Yellowstone Lake, Yellowstone National Park, Wyoming. Geobiology 8: 327–336.

2. Clingenpeel, S., R. E. Macur, J. Kan, W. P. Inskeep, D. Lovalvo, J. Varley, E. Mathur, K. Nealson, Y. Gorby, H. Jiang, T. LaFracois, and T. R. McDermott. 2011. Yellowstone Lake: high energy geochemistry and rich bacterial diversity. Environmental Microbiology 13: 2172–2185.  

3. Kan, J., S. R. Clingenpeel, R. E. Macur, W. P. Inskeep, D. Lovalvo, J. Varley, Y. Gorby, T. R. McDermott, and K. Nealson. 2011. Archaea in Yellowstone Lake. ISME J 5: 1784–1795.

4. Clingenpeel, S. R., J. Kan, R. E. Macur, D. Lovalvo, J. Varley, Y. Gorby, W. P. Inskeep, K. Nealson, and T. R. McDermott. 2013. Yellowstone Lake Nanoarchaeota. Frontiers in Microbiology 4: 1–8.

5. Zhou, J., D. Sun, A. Childers, T. R. McDermott, Y. Wang, and M. R. Liles. 2014. Three novel virophage genomes discovered from Yellowstone Lake metagenomes. Journal of Virology 89: 1278–1285.

For further information:

Morgan, L. A., W. C. Shanks III, K. L. Pierce, D. A. Lovalvo, G. K. Lee, M. W. Webring, et al. 2007. The floor of Yellowstone Lake is anything but quiet – new discoveries from high resolution sonar imaging, seismic-reflection profiling, and submersible studies. In: Morgan, L. A. (Ed.), Integrated Geoscience Studies in the Greater Yellowstone Area – Volcanic, Tectonic, and Hydrothermal. Processes in the Yellowstone Geoecosystem. US Geological Survey Professional Paper 1717, p. 95–126.

Adams, D. K., D. J. McGillicuddy Jr., L. Zamudio, A. M. Thurnherr, X. Liang, O. Rouxel, C. R. German, L. S. Mullineaux. 2011. Surface-generated mesoscale eddies transport deep-sea products from hydrothermal vents. Science 332: 580–583.

Franke, M. A. 2013. Genetic Diversity in Yellowstone Lake: The Hot and Cold Spots. Yellowstone Science 21: 6–22.

Zhou, J. L., W.-J. Zhang, S.-L. Yan, J.-Z. Xiao, Y.-Y. Zhang, B.-L. Li, Y.-J. Pan, and Y.-J. Wang. 2013. Diversity of virophages in metagenomic data sets. Journal of Virology. 87: 4225–4236.

Other grants to Yellowstone Park Foundation (1)

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