Bacterial diversity and chemical ecology of natural product-producing bacteria from Great Salt Lake sediment

Great Salt Lake (GSL), located northwest of Salt Lake City, UT, is the largest terminal lake in the USA. While the average salinity of seawater is ~3.3%, the salinity in GSL ranges between 5% and 28%. In addition to being a hypersaline environment, GSL also contains toxic concentrations of heavy metals, such as arsenic, mercury, and lead. The extreme environment of GSL makes it an intriguing subject of study, both for its unique microbiome and its potential to harbor novel natural product-producing bacteria, which could be used as resources for the discovery of biologically active compounds. Though work has been done to survey and catalog bacteria found in GSL, the Lake's microbiome is largely unexplored, and little to no work has been done to characterize the natural product potential of GSL microbes. Here, we investigate the bacterial diversity of two important regions within GSL, describe the first genomic characterization of Actinomycetota isolated from GSL sediment, including the identification of two new Actinomycetota species, and provide the first survey of the natural product potential of GSL bacteria.

Genomic Diversity and Zoonotic Potential of Brucella neotomae

After reports in 2017 of Brucella neotomae infections among humans in Costa Rica, we sequenced 12 strains isolated from rodents during 1955-1964 from Utah, USA. We observed an exact strain match between the human isolates and 1 Utah isolate. Independent confirmation is required to clarify B. neotomae zoonotic potential.

Establishment of a Halophilic Bloom in a Sterile and Isolated Hypersaline Mesocosm

Extreme environments, including hypersaline pools, often serve as biogeographical islands. Putative colonizers would need to survive transport across potentially vast distances of inhospitable terrain. Hyperhalophiles, in particular, are often highly sensitive to osmotic pressure. Here, we assessed whether hyperhalophiles are capable of rapidly colonizing an isolated and sterile hypersaline pool and the order of succession of the ensuing colonizers. A sterile and isolated 1 m3 hypersaline mesocosm pool was constructed on a rooftop in Charleston, SC. Within months, numerous halophilic lineages successfully navigated the 20 m elevation and the greater than 1 km distance from the ocean shore, and a vibrant halophilic community was established. All told, in a nine-month period, greater than a dozen halophilic genera colonized the pool. The first to arrive were members of the Haloarchaeal genus Haloarcula. Like a weed, the Haloarcula rapidly colonized and dominated the mesocosm community but were later supplanted by other hyperhalophilic genera. As a possible source of long-distance inoculum, both aerosol and water column samples were obtained from the Great Salt Lake and its immediate vicinity. Members of the same genus, Haloarcula, were preferentially enriched in the aerosol sample relative to the water column samples. Therefore, it appears that a diverse array of hyperhalophiles are capable of surviving aeolian long-distance transport and that some lineages, in particular, have possibly adapted to that strategy.

Nest success of ground-nesting ducks in the wetlands of Great Salt Lake, Utah

The number of ground-nesting ducks in the wetlands of Great Salt Lake, Utah has drastically decreased in the past few decades. A potential cause for this decline is the increase of predator species and their abundances, which has caused most nests to fail from depredation. Ground-nesting ducks may be able to reduce the risk of nest depredation by selecting nest sites where local physical structures or vegetation provides olfactory or visual concealment. To test this, we used logistic exposure models to look at the effect of nest-site characteristics on daily survival rates (DSRs) of nests during 2019, 2020, and 2021 in the wetlands of Great Salt Lake, Utah. We found 825 duck nests including 458 cinnamon teal (Spatula cyanoptera), 166 mallards (Anas platyrhynchos), and 201 gadwalls (Mareca strepera). DSRs were 0.9714 ± 0.0019 in 2019, 0.9282 ± 0.0049 in 2020, and 0.8274 ± 0.0185 in 2021. Survival rates varied among years but not among duck species. Striped skunks (Mephitis mephitis) and raccoons (Procyon lotor) were responsible for 85% of depredated nests. Nests located near other duck nests had higher DSRs than more dispersed nests. Neither visual nor olfactory characteristics correlated with increased DSRs based on AIC_c analysis. Nests located inside a mixed nesting colony of American avocets (Recurvirostra americana), black-necked stilts (Himantopus mexicanus), and common terns (Sterna hirundo) had higher DSRs than duck nests outside the colony. Increased nesting densities of ducks and other colonial waterbirds had the greatest impact on nesting success. Increased nest density may be encouraged through early spring green-up.

Industrial Particulate Pollution and Historical Land Use Contribute Metals of Concern to Dust Deposited in Neighborhoods Along the Wasatch Front, UT, USA

The Salt Lake Valley, UT, USA, is proximal to the desiccating Great Salt Lake (GSL). Prior work has found that this lakebed/playa contributes metals-laden dust to snow in the Wasatch and Uinta Mountains. Dust and industrial particulate pollution are also delivered to communities along the Wasatch Front, but their sources, compositions, and fluxes are poorly characterized. In this study, we analyzed the dust deposited in 18 passive samplers positioned near the GSL, in cities in and near the Salt Lake Valley for total dust flux, the <63 µm dust fraction, ⁸⁷Sr/⁸⁶Sr, and trace element geochemistry. We compared spatial patterns in metal flux and abundance with community-level socioeconomic metrics. We observed the highest dust fluxes at sites near the GSL playa. Within the urban corridor, ⁸⁷Sr/⁸⁶Sr and trace element relative abundances suggest that most of the dust to which people are regularly exposed may be fugitive dust from local soil materials. The trace metal content of dust deposited along the Wasatch Front exceeded Environmental Protection Agency screening levels and exhibited enrichment relative to both the upper continental crust and the dust collected adjacent to GSL. Sources of metals to dust deposited along the Wasatch Front may include industrial activities like mining, oil refining, as well as past historical pesticide and herbicide applications. Arsenic and vanadium indicated a statistically significant positive correlation with income, whereas lead, thallium, and nickel exhibited higher concentrations in the least wealthy and least white neighborhoods.

Unexpected Abundance and Diversity of Phototrophs in Mats from Morphologically Variable Microbialites in Great Salt Lake, Utah

Microbial mat communities are associated with extensive (∼700 km²) and morphologically variable carbonate structures, termed microbialites, in the hypersaline Great Salt Lake (GSL), Utah. However, whether the composition of GSL mat communities covaries with microbialite morphology and lake environment is unknown. Moreover, the potential adaptations that allow the establishment of these extensive mat communities at high salinity (14% to 17% total salts) are poorly understood. To address these questions, microbial mats were sampled from seven locations in the south arm of GSL representing different lake environments and microbialite morphologies. Despite the morphological differences, microbialite-associated mats were taxonomically similar and were dominated by the cyanobacterium Euhalothece and several heterotrophic bacteria. Metagenomic sequencing of a representative mat revealed Euhalothece and subdominant Thiohalocapsa populations that harbor the Calvin cycle and nitrogenase, suggesting they supply fixed carbon and nitrogen to heterotrophic bacteria. Fifteen of the next sixteen most abundant taxa are inferred to be aerobic heterotrophs and, surprisingly, harbor reaction center, rhodopsin, and/or bacteriochlorophyll biosynthesis proteins, suggesting aerobic photoheterotrophic (APH) capabilities. Importantly, proteins involved in APH are enriched in the GSL community relative to that in microbialite mat communities from lower salinity environments. These findings indicate that the ability to integrate light into energy metabolism is a key adaptation allowing for robust mat development in the hypersaline GSL.IMPORTANCE The earliest evidence of life on Earth is from organosedimentary structures, termed microbialites, preserved in 3.481-billion-year-old (Ga) rocks. Phototrophic microbial mats form in association with an ∼700-km² expanse of morphologically diverse microbialites in the hypersaline Great Salt Lake (GSL), Utah. Here, we show taxonomically similar microbial mat communities are associated with morphologically diverse microbialites across the lake. Metagenomic sequencing reveals an abundance and diversity of autotrophic and heterotrophic taxa capable of harvesting light energy to drive metabolism. The unexpected abundance of and diversity in the mechanisms of harvesting light energy observed in GSL mat populations likely function to minimize niche overlap among coinhabiting taxa, provide a mechanism(s) to increase energy yield and osmotic balance during salt stress, and enhance fitness. Together, these physiological benefits promote the formation of robust mats that, in turn, influence the formation of morphologically diverse microbialite structures that can be imprinted in the rock record.

A management case study for a new commercial fishery: brine shrimp harvesting in Great Salt Lake, Utah, USA

A fishery for brine shrimp (Artemia franciscana) cysts to supply the aquaculture industry considerably expanded in the late 1980s in the Great Salt Lake, Utah, USA. With this expansion, concerns emerged in the 1990s about the fishery's sustainability, especially its impact on the abundant western North American waterbirds that use the lake and feed on brine shrimp. We track the development of management strategies using adaptive management by the Utah Division of Wildlife Resources (UDWR), which focused on the biology of the system and development of biology-based harvesting models. The models and their rationale are presented, their success in forecasting is evaluated, and implications for managing the harvest and conserving waterbirds are examined. We view this as an interesting case study because it transpired over a short time in a relatively simple system. This permitted us to clearly track management from the onset of a harvest market, through realization that the harvest had to be managed in the absence of needed biological knowledge, to the adaptive development of management strategies as biological knowledge was accumulated. The outcome illustrates the success that harvest management can attain with careful monitoring of the resource and terminating the harvest when a necessary escapement stock is attained.

Effects of salinity on microbialite-associated production in Great Salt Lake, Utah

Microbialites, organosedimentary carbonate structures, cover approximately 20% of the basin floor in the south arm of Great Salt Lake, which ranges from ~12 to 15% salinity. Photosynthetic microbial mats associated with these benthic mounds contribute biomass that supports secondary production in the ecosystem, including that of the brine shrimp, Artemia franciscana. However, the effects of predicted increases in the salinity of the lake on the productivity and composition of these mats and on A. franciscana fecundity is not well documented. In the present study, we applied molecular and microcosm-based approaches to investigate the effects of changing salinity on (1) the primary productivity, abundance, and composition of microbialite-associated mats of GSL, and (2) the fecundity and survivability of the secondary consumer, A. franciscana. When compared to microcosms incubated closest to the in situ measured salinity of 15.6%, the abundance of 16S rRNA gene templates increased in microcosms with lower salinities and decreased in those with higher salinities following a 7-week incubation period. The abundance of 16S rRNA gene sequences affiliated with dominant primary producers, including the cyanobacterium Euhalothece and the diatom Navicula, increased in microcosms incubated at decreased salinity, but decreased in microcosms incubated at increased salinity. Increased salinity also decreased the rate of primary production in microcosm assays containing mats incubated for 7 weeks and decreased the number of A. franciscana cysts that hatched and survived. These results indicate that an increase in the salinity of GSL is likely to have a negative impact on the productivity of microbialite communities and the fecundity and survivability of A. franciscana. These observations suggest that a sustained increase in the salinity of GSL and the effects this has on primary and secondary production could have an upward and negative cascading effect on higher-trophic-level ecological compartments that depend on A. franciscana as a food source, including a number of species of migratory birds.

The cost of addressing saline lake level decline and the potential for water conservation markets

The world's saline lakes are shrinking and human water diversions are a significant contributor. While there is increased interest in protecting the ecosystem services provided by these lakes, the cost of protecting water levels has not been estimated. To explore this question we consider the case of Great Salt Lake (Utah, USA) where human diversions from three rivers have caused the lake level to decline during the last century. Recent work has suggested the restoration of inflows is necessary to maintain a target elevation consistent with well-functioning ecosystems. We construct cost estimates of increasing water inflows using conservation cost curves for each river basin. We then compare the cost of uniform cutbacks to cap-and-trade systems which allow intra- and inter-basin trading. The cost of water to permanently implement uniform water right cutbacks to increase inflows by 20% above current levels is $37.4 million. Costs and cost-savings are sensitive to alternative allocation, inflow, and cost assumptions, and we estimate significant cost reductions from intra-basin water conservation markets (5-54% cost decrease) and inter-basin water conservation markets (22-57% cost decrease).

Great Salt Lake microbiology: a historical perspective

Over geologic time, the water in the Bonneville basin has risen and  fallen, most dramatically as freshwater Lake Bonneville lost enormous volume 15,000-13,000 years ago and became the modern day Great Salt Lake. It is likely that paleo-humans lived along the shores of this body of water as it shrunk to the present margins, and native peoples inhabited the surrounding desert and wetlands in recent times. Nineteenth century Euro-American explorers and pioneers described the geology, geography, and flora and fauna of Great Salt Lake, but their work attracted white settlers to Utah, who changed the lake immeasurably. Human intervention in the 1950s created two large sub-ecosystems, bisected by a railroad causeway. The north arm approaches ten times the salinity of sea water, while the south arm salinity is a meager four times that of the oceans. Great Salt Lake was historically referred to as sterile, leading to the nickname "America's Dead Sea." However, the salty brine is teaming with life, even in the hypersaline north arm. In fact, scientists have known that this lake contains a diversity of microscopic lifeforms for more than 100 years. This essay will explore the stories of the people who observed and researched the salty microbiology of Great Salt Lake, whose discoveries demonstrated the presence of bacteria, archaea, algae, and protozoa that thrive in this lake. These scientists documented the lake's microbiology as the lake changed, with input from human waste and the creation of impounded areas. Modern work on the microbiology of Great Salt Lake has added molecular approaches and illuminated the community structures in various regions, and fungi and viruses have now been described. The exploration of Great Salt Lake by scientists describing these tiny inhabitants of the brine illuminate the larger terminal lake with its many facets, anthropomorphic challenges, and ever-changing shorelines.

Weather and eared grebe winter migration near the Great Salt Lake, Utah

This study provides insight from the use of weather radar observations to understand the characteristics of the eared grebe migration near the Great Salt Lake (GSL) and provides unique information on weather conditions connected to these migration events. Doppler weather radar measurements from the Salt Lake City, Utah WSR-88D radar site (KMTX), along with meteorological surface and rawinsonde data, were used to identify and examine 281 eared grebe migration events across 15 winters from 1997/1998 through 2011/2012. An average of about 19 migration events occurred each winter with considerable interannual variability, as well as large variance in the spatial area and number of birds departing the GSL during each event. The migration events typically occurred during clear sky conditions in the presence of surface high pressure and colder than average surface temperatures. Migration events began 55 min after sunset, on average across the winter seasons, and in one case we demonstrate that an extended, nonstop flight was initiated of the departing eared grebes to northern Mexico. Eared grebes leaving the GSL largely flew above the freezing level with a mean northerly tailwind at flight altitude of 3.1 m s^-1 and a westerly, cross-flight wind of 5.0 m s^-1 while having an average flight speed at cruising altitude of 16.9 m s^-1, or 61 km h^-1. In addition to determining the variability of meteorological conditions during migration events across the 15 winters, atmospheric conditions during the largest migration event observed are presented and discussed.

Differential Gene Expression in Response to Salinity and Temperature in a Haloarcula Strain from Great Salt Lake, Utah

Haloarchaea that inhabit Great Salt Lake (GSL), a thalassohaline terminal lake, must respond to the fluctuating climate conditions of the elevated desert of Utah. We investigated how shifting environmental factors, specifically salinity and temperature, affected gene expression in the GSL haloarchaea, NA6-27, which we isolated from the hypersaline north arm of the lake. Combined data from cultivation, microscopy, lipid analysis, antibiotic sensitivity, and 16S rRNA gene alignment, suggest that NA6-27 is a member of the Haloarcula genus. Our prior study demonstrated that archaea in the Haloarcula genus were stable in the GSL microbial community over seasons and years. In this study, RNA arbitrarily primed PCR (RAP-PCR) was used to determine the transcriptional responses of NA6-27 grown under suboptimal salinity and temperature conditions. We observed alteration of the expression of genes related to general stress responses, such as transcription, translation, replication, signal transduction, and energy metabolism. Of the ten genes that were expressed differentially under stress, eight of these genes responded in both conditions, highlighting this general response. We also noted gene regulation specific to salinity and temperature conditions, such as osmoregulation and transport. Taken together, these data indicate that the GSL Haloarcula strain, NA6-27, demonstrates both general and specific responses to salinity and/or temperature stress, and suggest a mechanistic model for homeostasis that may explain the stable presence of this genus in the community as environmental conditions shift.

Potential for Waterborne and Invertebrate Transmission of West Nile Virus in the Great Salt Lake, Utah

In November and December of 2013, a large mortality event involving 15,000 to 20,000 eared grebes (Podiceps nigricollis) occurred at the Great Salt Lake (GSL), UT. The onset of the outbreak in grebes was followed by a mortality event in >86 bald eagles (Haliaeetus leucocephalus). During the die-off, West Nile virus (WNV) was detected by reverse transcription-PCR (RT-PCR) or viral culture in the carcasses of grebes and eagles submitted to the National Wildlife Health Center. However, no activity of mosquitoes, the primary vectors of WNV, was detected by the State of Utah's WNV monitoring program. The transmission of WNV has rarely been reported during the winter in North America in the absence of known mosquito activity; however, the size of this die-off, the habitat in which it occurred, and the species involved are unique. We experimentally investigated whether WNV could survive in water with a high salt content, as found at the GSL, and whether brine shrimp, the primary food of migrating eared grebes on the GSL, could have played a role in the transmission of WNV to feeding birds. We found that WNV can survive up to 72 h at 4°C in water containing 30 to 150 ppt NaCl, and brine shrimp incubated with WNV in 30 ppt NaCl may adsorb WNV to their cuticle and, through feeding, infect epithelial cells of their gut. Both mechanisms may have potentiated the WNV die-off in migrating eared grebes on the GSL.IMPORTANCE Following a major West Nile virus die-off of eared grebes and bald eagles at the Great Salt Lake (GSL), UT, in November to December 2013, this study assessed the survival of West Nile virus (WNV) in water as saline as that of the GSL and whether brine shrimp, the major food for migrating grebes, could have played a role as a vector for the virus. While mosquitoes are the major vector of WNV, under certain circumstances, transmission may occur through contaminated water and invertebrates as food.

Bonnevillamides, Linear Heptapeptides Isolated from a Great Salt Lake-Derived Streptomyces sp

Streptomyces sp. GSL-6B was isolated from sediment collected from the Great Salt Lake and investigation of its organic extract led to the isolation of three new linear heptapeptides, bonnevillamides A (1), B (2), and C (3). The bonnevillamides represent a new class of linear peptides featuring unprecedented non-proteinogenic amino acids. All three peptides contain the newly characterized bonnevillic acid moiety (3-(3,5-dichloro-4-methoxyphenyl)-2-hydroxyacrylic acid), as well as a heavily modified proline residue. Moreover, in bonnevillamide A, the terminal proline residue found in bonnevillamides B and C is replaced with 4-methyl-azetidine-2-carboxylic acid methyl ester. The structures of the three heptapeptides were elucidated by NMR, high-resolution electrospray ionization mass spectroscopy (HRESIMS), and LC-MS/MS, and the absolute configuration of all proteinogenic amino acid residues were determined by advanced Marfey’s method. Bonnevillamides A, B and C were evaluated for their effects on zebrafish embryo development. All three heptapeptides were shown to modulate heart growth and cardiac function, with bonnevillamide B having the most pronounced effect.

Bacterial Dormancy Is More Prevalent in Freshwater than Hypersaline Lakes

Bacteria employ a diverse array of strategies to survive under extreme environmental conditions but maintaining these adaptations comes at an energetic cost. If energy reserves drop too low, extremophiles may enter a dormant state to persist. We estimated bacterial dormancy and identified the environmental variables influencing our activity proxy in 10 hypersaline and freshwater lakes across the Western United States. Using ribosomal RNA:DNA ratios as an indicator for bacterial activity, we found that the proportion of the community exhibiting dormancy was 16% lower in hypersaline than freshwater lakes. Based on our indicator variable multiple regression results, saltier conditions in both freshwater and hypersaline lakes increased activity, suggesting that salinity was a robust environmental filter structuring bacterial activity in lake ecosystems. To a lesser degree, higher total phosphorus concentrations reduced dormancy in all lakes. Thus, even under extreme conditions, the competition for resources exerted pressure on activity. Within the compositionally distinct and less diverse hypersaline communities, abundant taxa were disproportionately active and localized in families Microbacteriaceae (Actinobacteria), Nitriliruptoraceae (Actinobacteria), and Rhodobacteraceae (Alphaproteobacteria). Our results are consistent with the view that hypersaline communities are able to capitalize on a seemingly more extreme, yet highly selective, set of conditions and finds that extremophiles may need dormancy less often to thrive and survive.

Calculating salt loads to Great Salt Lake and the associated uncertainties for water year 2013; updating a 48 year old standard

Effective management of surface waters requires a robust understanding of spatiotemporal constituent loadings from upstream sources and the uncertainty associated with these estimates. We compared the total dissolved solids loading into the Great Salt Lake (GSL) for water year 2013 with estimates of previously sampled periods in the early 1960s. We also provide updated results on GSL loading, quantitatively bounded by sampling uncertainties, which are useful for current and future management efforts. Our statistical loading results were more accurate than those from simple regression models. Our results indicate that TDS loading to the GSL in water year 2013 was 14.6 million metric tons with uncertainty ranging from 2.8 to 46.3 million metric tons, which varies greatly from previous regression estimates for water year 1964 of 2.7 million metric tons. Results also indicate that locations with increased sampling frequency are correlated with decreasing confidence intervals. Because time is incorporated into the LOADEST models, discrepancies are largely expected to be a function of temporally lagged salt storage delivery to the GSL associated with terrestrial and in-stream processes. By incorporating temporally variable estimates and statistically derived uncertainty of these estimates, we have provided quantifiable variability in the annual estimates of dissolved solids loading into the GSL. Further, our results support the need for increased monitoring of dissolved solids loading into saline lakes like the GSL by demonstrating the uncertainty associated with different levels of sampling frequency.

The ecology of Dunaliella in high-salt environments

Halophilic representatives of the genus Dunaliella, notably D. salina and D. viridis, are found worldwide in salt lakes and saltern evaporation and crystallizer ponds at salt concentrations up to NaCl saturation. Thanks to the biotechnological exploitation of D. salina for β-carotene production we have a profound knowledge of the physiology and biochemistry of the alga. However, relatively little is known about the ecology of the members of the genus Dunaliella in hypersaline environments, in spite of the fact that Dunaliella is often the main or even the sole primary producer present, so that the entire ecosystem depends on carbon fixed by this alga. This review paper summarizes our knowledge about the occurrence and the activities of different Dunaliella species in natural salt lakes (Great Salt Lake, the Dead Sea and others), in saltern ponds and in other salty habitats where members of the genus have been found.