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Saline lakes are known to be sensitive to changes in environmental conditions on a broad temporal scale. Therefore, variations in the mineralogical, geochemical, and sedimentological characteristics of these settings have often been interpreted to reflect oscillations in climatic conditions. However, recent work has shown that microbial communities can also influence the formation of carbonate and evaporite minerals in saline lake environments, especially in the salars of South America. Here, both abiotic and organomineralization pathways can be found to exist within the same salar environments, indicating a high degree of spatial heterogeneity of mineralization processes in such settings. Thus, the drivers of the resulting mineral assemblage can be complicated to disentangle through space and time. A process-level understanding of first-order controls on mineral assemblages can provide new insights into sedimentological dynamics of salar environments.Babel (2004) published a conceptual model based on marine-fed systems that established links between salinity and the style of gypsum mineral deposition. Based on field and laboratory analyses conducted on sediments in the Salar de Llamara, we adapted this model for a continental saline lake setting (Reid et al., 2021). In the present study, we aimed to test whether our salar-scale conceptual model was applicable more generally to continental saline lake environments. To accomplish this goal, we investigated a 15-year time series of electrical conductivity, a proxy for salinity, collected in five saline lake/wetland systems situated along the margin of the Salar de Atacama. Based on this dataset, we predicted the style and mineralogy of mineral deposition in each setting using our salar-scale conceptual model. Next, we compared our predictions with published field descriptions of the occurrences of biofilms, microbial mats, microbialites, and evaporite deposits in these lakes. Through a principal component analysis, we evaluated environmental characteristics such as electrical conductivity, pH, and dissolved oxygen as controls on mineral morphology and mineralogy.Results indicate that salinity is a first-order control on sedimentological expression in the lakes of the Salar de Atacama, although the transition between organomineralization pathways and physicochemical precipitation may occur at different salinity values than observed in other saline lake settings. Broadly in agreement with our model from the Salar de Llamara, granular precipitates of carbonate minerals formed within microbial mats were associated with environments characterized by low salinity, while microbial mats with laminated precipitates were found in settings with moderate salinity in the Salar de Atacama. High salinity environments contained crystalline bottom types characterized by selenitic morphology. Because some South American salars have been cited as living laboratories analogous to the ancient conditions that fostered the evolution of terrestrial and Martian life, these insights into mineralization are important. Improved constraints on the controls of carbonate and evaporite mineral deposition in saline lake environments will elucidate the definition of habitable environments, and provide a testing ground for the production and preservation of chemical and morphological biosignatures through time.

Although thought to be high-resolution archives of paleoenvironmental changes, subsurface sediments deposited in saline lakes situated in salar environments have rarely been studied. To address this knowledge gap, sediment cores of varying depths ranging from 0.42 to 2.2 meters were collected from four saline lakes along the eastern margin of the Salar de Atacama, Chile. Characterization included sedimentological descriptions of lithification, sedimentary structures (microbial mats and microbialites), and color, as well as discrete measurements of total organic carbon content. Radiocarbon analysis was conducted on organic matter in the sediments. The recovered subsurface lithologies were heterogenous in color, stratigraphic features, and age dates, especially when compared between the lakes. Intervals of coarser sediment in the Soncor system lakes Chaxa, Burros Muertos and Barros Negros, appeared to be crystalline and were likely precipitated during periods characterized by higher salinity lake waters. Sediment cores collected from the Soncor system were broadly characterized by low total organic carbon content and punctuated intervals of coarse grained material deeper in the core. In the core collected from Aguas de Quelana, variations in lithology and hardgrounds were commonly observed. In concert, these results suggest that the eastern periphery of the salar was impacted by changes in salinity and water depth as these wetland area experienced changes in extent as a result of changes in wet and dry periods. Radiocarbon dating conducted on organic matter sampled at 4 intervals from each core revealed ages that were significantly older than expected, possibly due to local reservoir effects and subsurface hydrological dynamics. There were five age reversals documented in the transect of cores suggesting that the sources of radiocarbon may have changed over time. Results indicate that the geologic records of saline lake environments are as heterogeneous through time as they are in space.

Despite the harsh environmental conditions in the world's oldest and driest desert, some salt flat or 'salar' environments in the Atacama Desert host standing bodies of water known as saline lakes. Evaporite minerals deposited within saline lakes result from the equilibrium of environmental, sedimentological, and biogeochemical processes that occur in the salar; consequently, these minerals are sensitive records of human activities and ecological, evolutionary, and geological changes. The objective of this study was to evaluate feedbacks between physical, chemical, and microbial processes that culminate in distinct trends in brine chemistry, saline lake morphology, and associated evaporite sediments. Using samples from the Puquios of the Salar de Llamara, Atacama Desert, northern Chile, an analysis of spatial gradients and vertical stratification of lake elemental chemistry and mineral saturation indices were integrated with a comprehensive analysis of lake morphology, including depth, slope gradient, substrate type, and mineralogy. Lake waters ranged from saline to hypersaline, and exhibited normal, well mixed and inverse stratification patterns, and results suggest a correlation with lake morphology in the Salar de Llamara. Saline to hypersaline lakes (150 mS/cm) with stratified brines tended to have crystalline substrate and deep (35 cm) and steep-sided lake morphologies, while unstratified lakes with lower electrical conductivity (90 mS/cm and microbial substrates had gentle slopes and characteristically shallow depths (30 cm). Differences in minor element chemistry (Mn and Sr) between saline lakes were observed on scales of meters to kilometers, and result in different accessory mineral assemblages. Quantification of the physical, chemical, and microbial feedbacks that produce the observed heterogeneity in these ecosystems provides key insight into the geochemical composition and lake morphology of saline lakes in extreme environments around the world.

Humans may be exposed to microbial pathogens at recreational beaches via environmental sources, such as water, sand, and aerosols. Although infectious disease risk from exposure to waterborne pathogens has been an active area of research for decades, sand is a relatively unexplored reservoir of pathogens and fecal indicator bacteria (FIB). Beach sand and water habitats provide unique advantages and challenges to pathogen introduction, growth, and persistence, as well as continuous exchange between habitats. Models of FIB and pathogen fate and transport in sandy beach habitats can help predict the risk of infectious disease from recreational water use, but filling knowledge gaps such as decay rates and potential for microbial growth in beach habitats is necessary for accurate modeling. Climatic variability, whether natural or anthropogenically-induced, adds complexity to predictive modeling, but may increase human exposure to waterborne pathogens via extreme weather events, warming of water bodies and sea level rise in many regions. The popularity of human recreational beach activities, combined with predicted climate change scenarios, could amplify the risk of human exposure to pathogens and related illnesses. Other global change trends such as increased population growth and urbanization are expected to exacerbate contamination events and the predicted impacts of increasing levels of waterborne pathogens on human health. Such changes will alter microbial population dynamics in beach habitats, and will consequently affect the assumptions and relationships used in population models and quantitative microbial risk assessment (QMRA). Here, we discuss the literature on microbial population and transport dynamics in sand-water continuum habitats at beaches, how these dynamics can be modeled, and how climate change and other anthropogenic influences (e.g., land use, urbanization) should be considered when using and developing more holistic, beachshed-based models.

Anthropogenic climate change compromises reef growth as a result of increasing temperatures and ocean acidification. Scleractinian corals vary in their sensitivity to these variables, suggesting species composition will influence how reef communities respond to future climate change. Because data are lacking for many species, most studies that model future reef growth rely on uniform scleractinian calcification sensitivities to temperature and ocean acidification. In order to address this knowledge gap, calcification of twelve common and understudied Caribbean coral species was measured for two months under crossed temperatures (27°C, 30.3°C) and CO2 partial pressures (pCO2) (400, 900, 1300 μatm). Mixed effects models of calcification for each species were then used to project community-level scleractinian calcification using Florida Keys reef composition data and IPCC AR5 ensemble climate model data. Three of the four most abundant species, Orbicella faveolata, Montastraea cavernosa, and Porites astreoides, had negative calcification responses to both elevated temperature and pCO2. In the business-as-usual CO2 emissions scenario, reefs with high abundances of these species had projected end-of-century declines in scleractinian calcification of >50% relative to present-day rates. Siderastrea siderea, the other most-common species, was insensitive to both temperature and pCO2 within the levels tested here. Reefs dominated by this species had the most stable end-of-century growth. Under more optimistic scenarios of reduced CO2 emissions, calcification rates throughout the Florida Keys declined

Despite the importance of oolitic depositional systems as indicators of climate and reservoirs of inorganic C, little is known about the microbial functional diversity, structure, composition, and potential metabolic processes leading to precipitation of carbonates. To fill this gap, we assess the metabolic gene carriage and extracellular polymeric substance (EPS) development in microbial communities associated with oolitic carbonate sediments from the Bahamas Archipelago. Oolitic sediments ranging from high-energy 'active' to lower energy 'non-active' and 'microbially stabilized' environments were examined as they represent contrasting depositional settings, mostly influenced by tidal flows and wave-generated currents. Functional gene analysis, which employed a microarray-based gene technology, detected a total of 12,432 of 95,847 distinct gene probes, including a large number of metabolic processes previously linked to mineral precipitation. Among these, gene-encoding enzymes for denitrification, sulfate reduction, ammonification, and oxygenic/anoxygenic photosynthesis were abundant. In addition, a broad diversity of genes was related to organic carbon degradation, and N2 fixation implying these communities has metabolic plasticity that enables survival under oligotrophic conditions. Differences in functional genes were detected among the environments, with higher diversity associated with non-active and microbially stabilized environments in comparison with the active environment. EPS showed a gradient increase from active to microbially stabilized communities, and when combined with functional gene analysis, which revealed genes encoding EPS-degrading enzymes (chitinases, glucoamylase, amylases), supports a putative role of EPS-mediated microbial calcium carbonate precipitation. We propose that carbonate precipitation in marine oolitic biofilms is spatially and temporally controlled by a complex consortium of microbes with diverse physiologies, including photosynthesizers, heterotrophs, denitrifiers, sulfate reducers, and ammonifiers.

Recolonization of enterococci, at a non-point source beach known to contain high background levels of bacteria, was studied after a full-scale beach renovation project. The renovation involved importation of new exogenous sand, in addition to infrastructure improvements. The study's objectives were to document changes in sand and water quality and to evaluate the relative contribution of different renovation activities towards these changes. These objectives were addressed: by measuring enterococci levels in the sand and fecal indicator bacteria levels (enterococci and fecal coliform) in the water, by documenting sediment characteristics (mineralogy and biofilm levels), and by estimating changes in observable enterococci loads. Analysis of enterococci levels on surface sand and within sediment depth cores were significantly higher prior to beach renovation (6.3 to 72 CFU/g for each sampling day) when compared to levels during and after beach renovation (0.8 CFU/g to 12 CFU/g) (p

Enterococci, recommended at the U.S. federal level for monitoring water quality at marine recreational beaches, have been found to reside and grow within beach sands. However, the environmental and ecological factors affecting enterococcal persistence remain poorly understood, making it difficult to determine levels of fecal pollution and assess human health risks. Here we document the presence of enterococci associated with beach sediment biofilms at eight south Florida recreational beaches. Enterococcal levels were highest in supratidal sands, where they displayed a nonlinear, unimodal relationship with extracellular polymeric secretions (EPS), the primary component of biofilms. Enterococcal levels peaked at intermediate levels of EPS, suggesting that biofilms may promote the survival of enterococci but also inhibit enterococci as the biofilm develops within beach sands. Analysis of bacterial community profiles determined by terminal restriction fragment length polymorphisms showed the bacterial communities of supratidal sediments to be significantly different from intertidal and subtidal communities; however, no differences were observed in bacterial community compositions associated with different EPS concentrations. Our results suggest that supratidal sands are a microbiologically unique environment favorable for the incorporation and persistence of enterococci within beach sediment biofilms.

Results from controlled in situ experimentation conducted on the leeward reef tract of Curacao, Netherlands Antilles, indicate that the coral Montastraea annularis exhibits a complex, yet consistent, cellular response to increasing sea surface temperature (SST) and decreasing irradiance. This was determined by simultaneously quantifying and tracking the tissue density of zooxanthellae and mucocytes using a novel technique that integrates the lectin histochemical stain wheat germ agglutinin (WGA) with high-resolution (200 nm) optical epifluorescence microscopy. Coral colonies growing at 6-m water depth (WD) and an irradiance of 100.2 ± 6.5 μmol m−2 s−1 were treated with a shading experiment for 11 days that reduced irradiance to 34.9 ± 6.6, 72.0 ± 7.0 and 90.1 ± 4.2 μmol m−2 s−1, respectively. While a significant decrease in the density of both zooxanthellae and mucocytes were observed at all shade levels, the largest reduction occurred between the natural non-shaded control (44,298 ± 3,242 zooxanthellae cm−2; 4,853 ± 346 mucocytes cm−2) and the highest shading level (13,982 ± 1,961 zooxanthallae cm−2; 2,544 ± 372.9 mucocytes cm−2). Colonies were also sampled during a seasonal increase in SST of 1.5°C, where the density of zooxanthellae was significantly lower (from 54,710 ± 1,755 to 34,322 ± 2,894 cells cm−2) and the density of mucocytes was significantly higher (from 6,100 ± 304 to 29,658 ± 3,937 cells cm−2). These observations of coral cellular response to environmental change provide evidence to support new hypotheses for coral survival and the complex role played by mucus in feeding, microbial associations and resilience to increasing SST.

Within the tropical marine study site of Guánica Bay, Puerto Rico, polychlorinated biphenyls (PCBs) are subjected to coastal and oceanic currents coupled with marine microbial and geochemical processes. To evaluate these processes a hydrodynamic model was developed to simulate the transport of PCBs within nearshore and offshore marine areas of Guánica Bay. Material transport and circulation information from the model were matched with measurements from samples collected from within the bay. These samples, consisting of both intertidal and submerged sediments, were analyzed for physical characteristics (organic carbon, grain size, and mineralogy), microbial characteristics (target bacteria levels and microbial community analyses), presence of PCBs, and PCB-degrading enzymes. Results show that the bay geometry and bathymetry limit the mixing of the extremely high levels of PCBs observed in the eastern portion of the bay. Bay bottom sediments showed the highest levels of PCBs and these sediments were characterized by high organic carbon content and finer grain size. Detectable levels of PCBs were also observed within sediments found along the shore. Microbes from the bay bottom sediments showed a greater relative abundance of microbes from the Chloroflexi, phylum with close phylogenetic associations with known anaerobic PCB-degrading organisms. Based on quantitative PCR measurement of the biphenyl dioxygenase gene, the intertidal sediments showed the greatest potential for aerobic PCB degradation. These results elucidate particular mechanisms of PCB’s fate and transport in coastal, tropical marine environments.

Fecal indicator microbes, such as enterococci, are often used to assess potential health risks caused by pathogens at recreational beaches. Microbe levels often vary based on collection time and sampling location. The primary goal of this study was to assess how spatial and temporal variations in sample collection, which are driven by environmental parameters, impact enterococci measurements and beach management decisions. A secondary goal was to assess whether enterococci levels can be predictive of the presence of Staphylococcus aureus, a skin pathogen. Over a ten-day period, hydrometeorologic data, hydrodynamic data, bather densities, enterococci levels, and S. aureus levels including methicillin-resistant S. aureus (MRSA) were measured in both water and sand. Samples were collected hourly for both water and sediment at knee-depth, and every 6 h for water at waist-depth, supratidal sand, intertidal sand, and waterline sand. Results showed that solar radiation, tides, and rainfall events were major environmental factors that impacted enterococci levels. S. aureus levels were associated with bathing load, but did not correlate with enterococci levels or any other measured parameters. The results imply that frequencies of advisories depend heavily upon sample collection policies due to spatial and temporal variation of enterococci levels in response to environmental parameters. Thus, sampling at different times of the day and at different depths can significantly impact beach management decisions. Additionally, the lack of correlation between S. aureus and enterococci suggests that use of fecal indicators may not accurately assess risk for some pathogens.

Enterococci are used to assess the risk of negative human health impacts from recreational waters. Studies have shown sustained populations of enterococci within sediments of beaches but comprehensive surveys of multiple tidal zones on beaches in a regional area and their relationship to beach management decisions are limited. We sampled three tidal zones on eight South Florida beaches in Miami-Dade and Broward counties and found that enterococci were ubiquitous within South Florida beach sands although their levels varied greatly both among the beaches and between the supratidal, intertidal and subtidal zones. The supratidal sands consistently had significantly higher (p < 0.003) levels of enterococci (average 40 CFU/g dry sand) than the other two zones. Levels of enterococci within the subtidal sand correlated with the average level of enterococci in the water (CFU/100mL) for the season during which samples were collected (r(s) = 0.73). The average sand enterococci content over all the zones on each beach correlated with the average water enterococci levels of the year prior to sand samplings (r(s) = 0.64) as well as the average water enterococci levels for the month after sand samplings (r(s) = 0.54). Results indicate a connection between levels of enterococci in beach water and sands throughout South Florida's beaches and suggest that the sands are one of the predominant reservoirs of enterococci impacting beach water quality. As a result, beaches with lower levels of enterococci in the sand had fewer exceedences relative to beaches with higher levels of sand enterococci. More research should focus on evaluating beach sand quality as a means to predict and regulate marine recreational water quality.