Microbial ecology of Keane Wonder Spring, Death Valley National Park

This research is focused on developing a better understanding of he physiological and phylogenetic diversity as well as environmental abundance of bacteria of the genus: Shewanella in selected desert ecosystems. Prior research from this laboratory has revealed that these bacteria are very abundant in sulfurand organic-rich aquatics habitats. We have selected a number of habitats for detailed investigation (cultivation, molecular ecology and relevant environmental chemistry) including the Tropicana Wash, spring in Death Valley, the lower Virgin River and possibly Big Soda Lame, Nevada

Investigating the origin of coprolites from three great basin caves

The study of coprolites (mummified feces) is a relatively new endeavor, which enables investigations of the health and diet of ancient people and provides some of the oldest evidence to date for the human habitation in North America (2). In this project, 18 coprolites were examined from archeological digs at three Great Basin caves: the Bonneville Estates Rockshelter (UT), Hidden Cave (NV), and Top of the Terrace Rockshelter (UT). The main objectives were: 1) to verify human origin through the presence of mitochondrial DNA (mtDNA) and 2) assuming human origin, characterize intestinal microflora of Native Americans prior to European contact. Primer sets specific for human mtDNA were employed to obtain products and establish human origin in general and Native American origin specifically (through SNP analysis). Initial microbiological efforts targeted the bacterial genus, Bacteroides, which tend to dominate gut flora in modern humans and thus is considered an ideal indicator for human fecal contamination (1,6). Primers targeting human-associated Bacteroides spp. strains were used in conjunction with human mtDNA results to further verify human origin. A major obstacle in this project, as might be expected, was damage to ancient DNA (aDNA). aDNA from coprolite samples is usually degraded into short fragments due to hydrolytic or oxidative damage, greatly reducing the possibility of long polymerase chain reaction (PCR) amplifications (4). The suggestion is that if large fragments are obtained from PCR, that the sample is most likely contaminated (3). To repair the fragmented aDNA, a technique termed reconstructive polymerization (RP) developed by Golenberg et al. (3) was applied. If these samples are found to be of human origin, it could provide an interesting lens into not only humans, but also the colonization of Western North America and beyond

Diversity of Estrogen Degrading Microorganisms in Las Vegas Wash and Lake Mead, Nevada, USA

Endocrine disrupting chemicals (EDCs) are a subject of intense research as more studies reveal their persistence in the environment and detrimental effects on wildlife. Steroid hormones, including the natural and synthetic estrogens estrone (E1), 17-beta-estradiol (E2) and 17- alpha-ethinyl estradiol (EE2), are among the most bioactive and have been detected at low concentrations in waterways downstream from wastewater treatment plants. Las Vegas Wash, a stream flowing into Lake Mead and fed primarily by treated wastewater, provides a unique experimental system in which to study the role microorganisms play in the fate and dispersal of these compounds in surface waters

Attempts to cultivate bacteria from deep subsurface aquifers and mountaintop plant communities

In the late 1990s, the limits of life were pushed even further when microorganisms were discovered thriving 2.5 km below the surface of the Earth in deep South African gold mines. These very simple communities were dominated by a single species of bacteria from within the phylum, Firmicutes. Desulforudis audaxviator remains unique to a sizeable portion of the South African deep subsurface. At depths below 2.5km, it comprises well over 99% of all organisms present, which presents a unique circumstance in which the environment has provided a natural pure culture. From this naturally occurring pure culture, environmental genomics was applied to obtain the complete D. audaxviatorgenome and thus it’s biological functions were established. This presents a unique opportunity to now attempt to grow a previously uncultured organism using its genome as a road map to design a specific cultivation approach for D. audaxviator. The genome combined with precise chemical analysis of its native environment has yielded invaluable insights such as the organism’s ability to form spores, to reduce sulfate, to fix nitrogen and use ammonia, along with many other unique traits all of which will lead to successful cultivation. Here we describe the genome-enabled cultivation of this to date uncultured microorganism

Baseline microbial characterizations of an imperiled aquatic diversity hotspot: Ash Meadows National Wildlife Refuge

Located in the discharge zone of the Death Valley Flow System, Ash Meadows National Wildlife Refuge is a spring-fed desert oasis and biodiversity hotspot about 90 miles northwest of Las Vegas. These critical wetlands are potentially threatened by groundwater pumping, exotic species invasions, and climate change. Although a major component of the lower food web, very little is known about the microbial makeup of this ecosystem. As a first step towards understanding the microbial and biogeochemical aspects of this system, a detailed molecular-based characterization of microbial communities, baseline chemistry, and physical characteristics of various springs of Ash Meadows will be conducted over the summer of 2009. Specifically, springs will be compared using DNA extraction followed by PCR amplification of the 16s rRNA gene, DNA fingerprinting, cultivation, and flow cytometric cell counting

Hiding in plain sight: the globally distributed bacterial candidate phylum PAUC34f

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Chen, M. L., Becraft, E. D., Pachiadaki, M., Brown, J. M., Jarett, J. K., Gasol, J. M., Ravin, N. V., Moser, D. P., Nunoura, T., Herndl, G. J., Woyke, T., & Stepanauskas, R. Hiding in plain sight: the globally distributed bacterial candidate phylum PAUC34f. Frontiers in Microbiology, 11, (2020): 376, doi: 10.3389/fmicb.2020.00376.Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while free-living lineages of PAUC34f are distinct and relatively abundant in a wide range of environments.This work was funded by the United States National Science Foundation grants 1460861 (REU site at Bigelow Laboratory for Ocean Sciences), 1441717, 1335810, and 1232982 to RS, and the Simons Foundation (Life Sciences Project Award ID 510023) to RS. NR was supported by the Ministry of Science and Higher Education of Russia. GH was supported by the Austrian Science Fund (FWF) project ARTEMIS (P28781-B21) and the European Research Council under the European Community’s Seventh Framework Program (FP7/2007-2013)/ERC (Grant Agreement No. 268595). JG was supported by Spanish project RTI2018-101025-B-I00. TW and JJ were funded by the U.S. Department of Energy, Joint Genome Institute, a DOE Office of Science User Facility supported under Contract No. DE-AC02-05CH11231

Using Water Chemistry, Isotopes and Microbiology to Evaluate Groundwater Sources, Flow Paths and Geochemical Reactions in the Death Valley Flow System, USA

AbstractSprings of Ash Meadows and Furnace Creek (near or in Death Valley, CA) have nearly constant flow, temperature, chemistry, and similar δ2H and δ18O signatures. These factors indicate shared water sources and/or analogous geochemical reactions along similar flow paths. DNA-based (16S rRNA gene) microbial diversity assessments further illuminate these relationships. Whereas, all Ash Meadows springs share related archaeal populations, variations in carbon-14 (Crystal Spring) and strontium isotopes, Na+, SO2-, and methane concentrations (Big Spring), correspond with microbial differences within and between the two discharge areas. Similar geochemical signatures linking Ash Meadows and Furnace Creek springs appear to support a distinct end member at Big Spring in Ash Meadows, which is also supported by coincident enrichment in microbial methanogens and methanotrophs. Conversely, DNA libraries from a deep carbonate well (878 m) located between Ash Meadows and Furnace Creek (BLM-1), indicate no shared microbial diversity between Ash Meadows or Furnace Creek springs

Long distance microbial transport in air: Global change implications

The first manifestations of global change will most likelv be observed in the Earth\u27s atmosphere. Changing wind patterns, for example, may effect the long distance dispersal of microor-g anisms. The overall objective of this research is to correlate molecular assessments of microbial community structure from cloud water and snow samples, obtained from DRI\u27s Storm Peak Laboratory atop Mt. Werner in Colorado, with atmospheric data and calculated air mass back trajectories. Our activities for summer of 2009 will be a focused proof-of-concept exercise to determine if intact microbial DNA and viable cells can be recovered from cloud water and alpine snow samples. Specific methods employed will include DNA extraction and PCR amplification of the bacterial 16s rRNA gene, community fingerprinting (T-RFLP), flow cytometric cell counting, and dilution plate counting

Patterns of in situ Mineral Colonization by Microorganisms in a ~60°C Deep Continental Subsurface Aquifer

The microbial ecology of the deep biosphere is difficult to characterize, owing in part to sampling challenges and poorly understood response mechanisms to environmental change. Pre-drilled wells, including oil wells or boreholes, offer convenient access, but sampling is frequently limited to the water alone, which may provide only a partial view of the native diversity. Mineral heterogeneity demonstrably affects colonization by deep biosphere microorganisms, but the connections between the mineral-associated and planktonic communities remain unclear. To understand the substrate effects on microbial colonization and the community response to changes in organic carbon, we conducted an 18-month series of in situ experiments in a warm (57°C), anoxic, fractured carbonate aquifer at 752 m depth using replicate open, screened cartridges containing different solid substrates, with a proteinaceous organic matter perturbation halfway through this series. Samples from these cartridges were analyzed microscopically and by Illumina (iTag) 16S rRNA gene libraries to characterize changes in mineralogy and the diversity of the colonizing microbial community. The substrate-attached and planktonic communities were significantly different in our data, with some taxa (e.g., Candidate Division KB-1) rare or undetectable in the first fraction and abundant in the other. The substrate-attached community composition also varied significantly with mineralogy, such as with two Rhodocyclaceae OTUs, one of which was abundant on carbonate minerals and the other on silicic substrates. Secondary sulfide mineral formation, including iron sulfide framboids, was observed on two sets of incubated carbonates. Notably, microorganisms were attached to the framboids, which were correlated with abundant Sulfurovum and Desulfotomaculum sp. sequences in our analysis. Upon organic matter perturbation, mineral-associated microbial diversity differences were temporarily masked by the dominance of putative heterotrophic taxa in all samples, including OTUs identified as Caulobacter, Methyloversatilis, and Pseudomonas. Subsequent experimental deployments included a methanogen-dominated stage (Methanobacteriales and Methanomicrobiales) 6 months after the perturbation and a return to an assemblage similar to the pre-perturbation community after 9 months. Substrate-associated community differences were again significant within these subsequent phases, however, demonstrating the value of in situ time course experiments to capture a fraction of the microbial assemblage that is frequently difficult to observe in pre-drilled wells