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At least 1,747 records · Page 97Linked to original sources
USGS2022

Using structured decision making to evaluate potential management responses to detection of dreissenid mussel (Dreissena spp.) environmental DNA

Environmental (e)DNA tools are sensitive and cost-effective for early detection of invasive species. However, the uncertainty associated with the interpretation of positive eDNA detections makes it challenging to determine appropriate natural resource management responses. Multiple sources of error can give rise to positive detections of eDNA in a sample when individuals of that species are not present at the site or a widespread infestation is not imminent. Acting on an erroneous eDNA inference could result in needless costs or reductions in desirable resources. Alternatively, failure to rapidly act on eDNA results that truly indicate invader presence could compound negative impacts and lead to high, long-term costs to manage infestations. We used a structured decision making (SDM) process, which incorporates tradeoffs and uncertainties, to evaluate appropriate response actions following hypothetical eDNA detections of invasive dreissenid mussel ( Dreissena spp.) eDNA in Jordanelle Reservoir, Utah (USA). We worked with decision-makers and stakeholders to identify objectives and discrete management action alternatives to assess consequences and tradeoffs. Alternatives ranged from no action to intensive and expensive control efforts. The best performing alternative was delayed containment described by immediate attempts to confirm the eDNA detections using non-molecular sampling techniques followed by mandatory watercraft exit inspections to prevent dreissenid mussel spread to regional water bodies. Non-molecular sampling increased public support for management by demonstrating a commitment to monitor the invasion state before action, whereas containment decreased likelihood of regional spread to other waters. Delayed containment had the lowest downside risk, and the highest upside gains relative to other alternative actions. Sensitivity analyses showed our results to be robust to parameter and outcome uncertainty.

Management of Biological Invasions↗
USGS2016

Inference of population structure and demographic history in Taxodium distichum , a coniferous tree in North America, based on amplicon sequence analysis

PREMISE OF THE STUDY: Studies of natural genetic variation can elucidate the genetic basis of phenotypic variation and the past population structure of species. Our study species, Taxodium distichum , is a unique conifer that inhabits the flood plains and swamps of North America. Morphological and ecological differences in two varieties, T. distichum var. distichum (bald cypress) and T. distichum var. imbricarium (pond cypress), are well known, but little is known about the level of genetic differentiation between the varieties and the demographic history of local populations. METHODS: We analyzed nucleotide polymorphisms at 47 nuclear loci from 96 individuals collected from the Mississippi River Alluvial Valley (MRAV), and Gulf Coastal populations in Texas, Louisiana, and Florida using high-throughput DNA sequencing. Standard population genetic statistics were calculated, and demographic parameters were estimated using a composite-likelihood approach. KEY RESULTS: Taxodium distichum in North America can be divided into at least three genetic groups, bald cypress in the MRAV and Texas, bald cypress in Florida, and pond cypress in Florida. The levels of genetic differentiation among the groups were low but significant. Several loci showed the signatures of positive selection, which might be responsible for local adaptation or varietal differentiation. CONCLUSIONS: Bald cypress was genetically differentiated into two geographical groups, and the boundary was located between the MRAV and Florida. This differentiation could be explained by population expansion from east to west. Despite the overlap of the two varieties’ ranges, they were genetically differentiated in Florida. The estimated demographic parameters suggested that pond cypress split from bald cypress during the late Miocene.

American Journal of Botany↗
USGS2020

A 'weight of evidence' approach to evaluating structural equation models

It is possible that model selection has been the most researched and most discussed topic in the history of both statistics and structural equation modeling (SEM). The reason for this is because selecting one model for interpretive use from amongst many possible models is both essential and difficult. The published protocols and advice for model evaluation and selection in SEM studies are complex and difficult to integrate with current approaches used in biology. Opposition to the use of p-values and decision thresholds has been voiced by the statistics community, yet certain phases of model evaluation have been historically tied to reliance on p-values. In this paper, I outline an approach to model evaluation, comparison and selection based on a weight-of-evidence paradigm. The details and proposed sequence of steps are illustrated using a real-world example. At the end of the paper, I briefly discuss the current state of knowledge and a possible direction for future studies.

One Ecosystem↗
USGS2021

A protocol for modelling generalised biological responses using latent variables in structural equation models

In this paper we consider the problem of how to quantitatively characterize the degree to which a study object exhibits a generalized response. By generalized response, we mean a multivariate response where numerous individual properties change in concerted fashion due to some internal integration. In latent variable structural equation modeling (LVSEM), we would typically approach this situation using a latent variable to represent a general property of interest (e.g., performance) and multiple observed indicator variables that reflect the specific features associated with that general property. While ecologists have used LVSEM in a number of cases, there is substantial potential for its wider application. One obstacle is that LV models can be complex and easily over-specified, degrading their value as a means of generalization. It can also be challenging to diagnose causes of misspecification and understand which model modifications are sensible. In this paper we present a protocol, consisting of a series of questions, designed to guide the researchers through the evaluation process. These questions address (1) theoretical development, (2) data requirements, (3) whether responses to perturbation are general, (4) unique reactions by individual measures, and (5) how far generality can be extended. For this illustration, we reference a recent study considering the potential consequences of maintaining biodiversity as part of agricultural management on the overall quality of grapes used for wine making. We extend our presentation to include the complexities that occur when there are multiple species with unique reactions.

One Ecosystem↗
USGS2022

General guidance for custom-built structural equation models

Structural Equation Modeling (SEM) represents a quantitative methodology for specifying and evaluating causal network hypotheses. The application of SEM typically involves the use of specialized software packages that implement estimation procedures and automate model checking and the output of summary results. There are times when the specification details an investigator wishes to implement to represent their data relationships are not supported by available SEM packages. In such cases, it may be desirable to develop and evaluate SE models “by hand”, using specialized regression tools. In this paper, I demonstrate a general approach to custom-built applications of SEM. The approach illustrated can be used for a wide array of specialized applications of non-linear, multi-level, and other custom specifications in SE models.

Maine↗
USGS2025

Using structural causal modeling to infer the effects of wildfire on foothill yellow-legged frog occurrence

Sierra Nevada ecosystems have been influenced by fire for millennia; however, increasing wildfire size and frequency may yield unforeseen consequences on wildlife populations and their distribution. Foothill yellow-legged frogs Rana boylii have declined in portions of their range and are considered a species of conservation concern. We surveyed streams for foothill yellow legged frogs in and near the 2021 Dixie Fire footprint using double-observer visual encounter surveys that incorporated time-to-detection methods, and used structural causal modeling to improve post-fire inference while lacking pre-fire data. We found that foothill yellow-legged frog probability of occurrence was 4.93 (95% equal-tailed interval = 0.52 – 160) times higher outside the footprint of the Dixie Fire than within it, though probability of occurrence was generally low within our sampling frame (ψ unburned = 0.21 [0.08 – 0.49]; ψ burned = 0.05 [0.002 – 0.28]). Measured environmental characteristics, however, were similar within and outside the fire footprint, and observed occupancy patterns might reflect the recent historical distribution of the frogs. Our study emphasizes the importance of site-specific pre-disturbance data when attempting to evaluate the causal effects of disturbances on wildlife. Although it remains to be seen how this species will fare in an increasingly frequent and intense fire regime, foothill yellow-legged frogs may tolerate some level of fire disturbance.

California↗
USGS2015

A crustal structure model of the Beaufort-Mackenzie Margin, southern Canada Basin

Canada and the United States collaborated in geophysical survey operations in the Amerasia Basin from 2007 to 2011 using the Canadian icebreaker CCGS Louis S. St. Laurent and the US icebreaker USCGC Healy. Over 15000 km of bathymetry, sub-bottom profiles, and 16-channel seismic reflection data were acquired over the Canada Basin and Alpha Ridge. Expendable sonobuoys were deployed to collect P-wave refraction and wide angle reflection data to define the regional velocity structure of the sedimentary successions. Although the new seismic profiles tie with existing GSC multichannel seismic lines on the Beaufort Shelf, water-bottom multiples obscure direct correlation of deeper stratigraphic horizons and (at best) basement is poorly imaged. We present a 2-D gravity and magnetic model for the southern Canada Basin margin and Beaufort-Mackenzie Basin integrating the new LSSL data with an existing deep crustal seismic reflection profile. The model crosses the slope region, where bathymetry shallows, base-of-sediments is deep, and basement is not imaged because of the water-bottom multiple. The density values used in the model are constrained by empirical relationships between velocity and density rock properties; however, magnetic susceptibility values are based on typical values for the inferred crustal lithologies. Velocity analyses of the new sonobuoy data provide constraints on the composition of the sediments, and enable quantitative mapping of continental, oceanic, and transitional domains within the Canada Basin. The 2-D gravity and magnetic forward model provides estimates for basement and Moho depths, the distribution and depths of magnetic sources, and visualization of the underlying crustal architecture controlling basin formation.

Conference Paper↗
USGS2013

Plausible combinations: An improved method to evaluate the covariate structure of Cormack-Jolly-Seber mark-recapture models

Mark-recapture models are extensively used in quantitative population ecology, providing estimates of population vital rates, such as survival, that are difficult to obtain using other methods. Vital rates are commonly modeled as functions of explanatory covariates, adding considerable flexibility to mark-recapture models, but also increasing the subjectivity and complexity of the modeling process. Consequently, model selection and the evaluation of covariate structure remain critical aspects of mark-recapture modeling. The difficulties involved in model selection are compounded in Cormack-Jolly- Seber models because they are composed of separate sub-models for survival and recapture probabilities, which are conceptualized independently even though their parameters are not statistically independent. The construction of models as combinations of sub-models, together with multiple potential covariates, can lead to a large model set. Although desirable, estimation of the parameters of all models may not be feasible. Strategies to search a model space and base inference on a subset of all models exist and enjoy widespread use. However, even though the methods used to search a model space can be expected to influence parameter estimation, the assessment of covariate importance, and therefore the ecological interpretation of the modeling results, the performance of these strategies has received limited investigation. We present a new strategy for searching the space of a candidate set of Cormack-Jolly-Seber models and explore its performance relative to existing strategies using computer simulation. The new strategy provides an improved assessment of the importance of covariates and covariate combinations used to model survival and recapture probabilities, while requiring only a modest increase in the number of models on which inference is based in comparison to existing techniques.

Open Journal Of Ecology↗
USGS2017

Impacts of mastication fuel treatments on California, USA, chaparral vegetation structure and composition

Mechanical fuel treatments are a primary pre-fire strategy for potentially mitigating the threat of wildland fire, yet there is limited information on how they impact shrubland ecosystems. Our goal was to assess the impact of mechanical mastication fuel treatments on chaparral vegetation and to determine the extent to which they emulate early post-fire succession. Mastication treatments significantly reduced the height and cover of woody vegetation and increased herbaceous cover and diversity. Non-native cover, density, and diversity were also significantly higher in masticated treatments. Comparisons with post-fire data from two studies showed that certain ephemeral post-fire endemics were absent or of limited occurrence from masticated plots in comparison to their abundance on adjacent burned plots. Structurally, masticated sites differed in the dense woody debris cover, whereas burned sites had little such ground cover. Regional comparison of masticated plots to previously published post-fire studies found that burned sites had greater cover, density, and diversity of native species. However, masticated sites and burned sites were broadly similar in distribution of different growth forms. Results from our study show that the use of mastication fuel treatments in chaparral are not in alignment with some resource conservation goals, but in some cases it is recognized that such sacrifice of natural resources may be an acceptable tradeoff to potentially mitigating fire hazard.

California↗
USGS2026

Improving offshore 3D splay fault geometries and slip histories using seismic data reprocessing and structural modeling

The goal of this project as written in the CRESCENT seed grant proposal was as follows: 1) reprocess selected profiles along strike from 45° to 48°N from the CASIE21 crustal-scale seismic data to obtain higher-resolution and higher-quality imaging of the uppermost 1-2 km of the accretionary wedge; 2) convert high-resolution USGS sparker seismic data from the time to depth domain to constrain near-surface fault geometries; 3) use kinematic modeling in the MOVE software to derive individual fault slip rates and per-event-displacements; and 4) work with the CFM group to create updated 3D models of identified faults based on the new data sources. At this stage, we have begun the reprocessing of the CASIE21 seismic reflection data (Carbotte et al., 2023). The time-migration reprocessing of the CASIE21 dataset has improved imaging of the near-surface structure by incorporating usable frequencies up to ~220 Hz, in contrast to the ~50 Hz maximum usable content in the currently available pre-stack depth migrated (PSDM) profiles (Fig. 1C). An example of the image quality gained through reprocessing is shown in Fig. 1, where the dominant wavelength of each reflector is reduced to ~10 m (Fig. 1B) from ~20 m in the existing PSDM product (Fig. 1A). The reprocessing work is still currently in progress. While the imaging in the shallow section has been much improved, reprocessing below the first multiple is still needed to create a seamless image from the plate boundary to the surface.

Final Report↗
USGS1997

Deep regional resistivity structure across the Carlin Trend

The genesis of gold deposits along the Carlin trend is not fully understood. Many of the significant mineral deposits in the Carlin trend were formed during the Tertiary as a result of interrelated high-angle basin-and-range faulting, intrusive igneous activity, and hydrothermal processes (Radtke, 1985). According to Shawe (1991), the linearity of the gold deposits along the Carlin trend and the sub-parallel Battle Mountain-Eureka trend suggests that deep-penetrating regional structures controlled the emplacement of magmas generated in the lower part of the crust or upper mantle, and either provided hydrothermal fluids or caused heating of ground waters that were responsible for transport and deposition of the gold ores. To investigate crustal processes that may have contributed to the genesis of gold deposits along the trend, a regional southwest to northeast profile of magnetotelluric (MT) soundings was acquired in 1996 (line MT-MT′, Fig. 1). Two-dimensional resistivity modeling of the MT profile is being used to place constraints on possible heat or magma sources and possible tectonic controls on the linear distribution of mineral deposits.

Book chapter↗
USGS1994

Magnetic and gravity constraints on forearc upper crustal structure and composition, offshore northeast Japan

Marine magnetic and gravity data from the northeast Japan forearc offer insight to the subsurface structure, density and magnetization from which geologic interpretations and tectonic reconstructions can be made. Positive marine magnetic anomalies, on-land geology, drill hole data, and 2-1/2-dimensional models reveal that Kitakami plutons and possibly their associated volcanic rocks constitute part of the modern forearc basement and lie 100-150 km further east than previously thought. A method to create magnetization and density contrast maps was employed to produce a three-dimensional picture of the forearc basement rock properties averaged over a 14-km thickness. -Author

Pacific Ocean↗
USGS2022

Understory structure and heterospecifics influence the occupancy of a ground-nesting species of conservation concern, the Canada Warbler

Forest structure and composition in eastern U.S. forests are changing because of forest regeneration after farmland abandonment, less frequent occurrence of severe disturbances, and climate change. Some of these changes may disproportionally affect birds that rely on gap dynamics or other forest canopy disturbances to create understory habitat. The Canada Warbler ( Cardellina canadensis ) is one such understory specialist that has undergone consistent declines. We assessed environmental and interspecific factors associated with Canada Warbler space use in its southern breeding distribution to understand potential causes of population declines and inform conservation efforts. We evaluated Canada Warbler occupancy from 840 point count surveys conducted in 2017 and 2018 at 470 unique locations (79% of locations surveyed in both years) throughout Monongahela National Forest, West Virginia, USA. We modeled Canada Warbler occupancy probability as a function of environmental variables and included Black-throated Blue Warbler ( Setophaga caerulescens ) and Hermit Thrush ( Catharus guttatus ) as interacting species because all three species exhibit similar habitat preferences. Canada Warblers were most likely to occur in areas with rhododendron ( Rhododendron maximum ) density > 0.27 stems/m² and within 3 m of riparian areas (streams and wetlands). They were also more likely to occur in mid-elevation (highest occupancy at 930 m) northern hardwood forests when Black-throated Blue Warblers were also present. Black-throated Blue Warblers were most likely to occupy mid-elevation sites with high shrub density, whereas Hermit Thrushes were more likely to occupy high-elevation, old-age forests. Potential management actions could focus on conserving riparian areas in northern hardwood forests, especially those with dense rhododendron thickets. Such potential actions could also be beneficial across the entire elevation range we explored within the region (500–1300 m). Canada Warblers may be benefiting from the recent spread of rhododendron habitats and northern hardwood forest types within West Virginia.

West Virginia↗
USGS2011

Structural and functional effects of herbicides on non-target organisms in aquatic ecosystems with an emphasis on atrazine

Herbicide use has increased dramatically around the world over the past 6 decades (Gianessi and Reigner, 2007). Few herbicides were in use in the 1950s. However, by 2001 approximately 1.14 billion kilograms of herbicides were applied globally for the control of undesireable vegetation in agricultural, silvicultural, lawncare, aquacultural, and irrigation/recreational water management activities (Kiely et al., 2004). Twenty-eight percent of the total mass of herbicides is applied in the United States, with the remaining 72 percent being applied elsewhere around the globe (Kiely et al., 2004). Herbicides represent 36% of global pesticide use, followed by insecticides (25%), fungicides (10%) and other chemical classes (Kiely et al., 2004). Agricultural production accounts for approximately 90% of herbicide use in the U.S. (Kiely et al., 2004). Gianessi and Reigner (2007) indicated that herbicides are routinely used on more than 90% of the area designated for large commercial crops including corn, soybeans, cotton, sugar beets, peanuts, and rice. Increased farm mechanization, technological advancements in production of inexpensive sources of inorganic nitrogen fertilizer (e.g., anhydrous ammonia), and conversion of forest, grassland, and wetland habitats to cropland has led to a tremendous increase in global food production over the past half-century. Herbicides have augmented advances in large-scale agricultural systems and have largely replaced mechanical and hand-weeding control mechanisms (Gianessi and Reigner, 2007). The wide-spread use of herbicides in agriculture has resulted in frequent chemical detections in surface and groundwaters (Gilliom, 2007). The majority of herbicides used are highly water soluble and are therefore prone to runoff from terrestrial environments. In additon, spray drift and atmospheric deposition can contribute to herbicide contamination of aquatic environments. Lastly, selected herbicides are deliberately applied to aquatic environments for controlling nuisance aquatic vegetation. Although aquatic herbicide exposure has been widely documented, these exposures are not necessarily related to adverse non-target ecological effects on natural communities in aquatic environments. This chapter evaluates the potential for effects of herbicides on the structure and function of aquatic envrionments at the population, community, and ecosystem levels of biological organization. In this manuscript I examine several critical aspects of the subject matter area: primary herbicides in use and chemical modes of action; the regulatory process used for registration and risk assessment of herbicides; data regarding non-target risks and the relative sensitivity of aquatic plants, inveretebrates, and fish to herbicides; and emerging areas of science regarding the potential for endocrine-disrupting effects of herbicides on aquatic vertebrates. Much of the focus of this paper is on atrazine due to the extensive database which exists regarding its fate and effects.

Book chapter↗
USGS2026

A snapshot of Joshua tree (Yucca brevifolia and Y. jaegeriana) stand structure in the eastern Mojave Desert of California

The long-term viability of the iconic Joshua tree of the Mojave Desert is being evaluated. In 2022, we measured the abundance and heights of Joshua tree stems on 62 1000 m2 plots in the eastern Mojave Desert of California. The 2022 plots were represented by 33 plots in a population of western Joshua trees (Yucca brevifolia) and 29 plots in a population of eastern Joshua trees (Y. jaegeriana). Five plots had no Joshua trees; two of which in the western Joshua tree population were destroyed by fire. The 57 plots with Joshua trees supported 627 stems ranging from stems less than 25 cm to mature trees. The plots were examined by abundance and four size classes of the stems, as indicated by their height and indicative of their reproductive status. The western Joshua tree population had more stems (407) than the eastern population (220 stems) although the median difference was not significant. The western population had significantly more stems in pre-reproductive size classes, juvenile (> 25 cm to one-meter, p = 0.001) and sub_adult (> one- to two-meters, p = 0.001), than the eastern population but significantly fewer adult (> two-meters, p < 0.001) stems. The eastern population had significantly greater mean height of adult trees (302 cm +/- 75.3 cm) than the western population (263 cm +/- 52.9 cm) and a larger proportion of stems taller than two-meters (56%) than the western population (39%). In contrast, the western population has 77% of its population in younger size classes (> 25 cm to < 2 meters). These abundance and size class measures alone do not predict whether either population has sufficient natural stand regeneration for long term persistence, but the younger size class structure of the western population suggests greater long-term resilience than for the eastern population.

BioRxiv↗
USGS2026

Columbia Basin pygmy rabbit recovery planning through structured decision making

The endangered Columbia Basin pygmy rabbit (CBPR) faces multiple threats, particularly increasing risk of larger and more intense wildfires due to climate change, emerging disease, and sagebrush habitat loss due to agriculture and development. Through the use of conservation breeding, the CBPR wild population grew from a low of 16 individuals captured in 2001 to over 100 individuals in two subpopulations in 2024. However, these subpopulations are geographically proximate, with potential risk that both subpopulations could be affected by a single wildfire or disease event. Additionally, a succession of setbacks in the breeding program has prompted a natural re-evaluation point for the CBPR conservation program. We undertook a structured decision-making (SDM) process with participants from both Washington Department of Fish and Wildlife (WDFW) and US Fish and Wildlife Service (USFWS) to develop a strategy that is sustainable and implementable for guiding management in the coming decades across the range of the CBPR, taking into account changing conditions and updated information. A population model that incorporated both demographic and high impact event uncertainties was developed to test how alternative strategies – defined by conservation breeding program, vaccination, and translocation components – affect CBPR population growth and cost objectives. Based on analysis of the model results, we identified the following actions that appear to have the greatest potential to allow WDFW and USFWS to meet their conservation objectives for CBPR: Continue conservation breeding program, and possibly expand to include an island subpopulation (an isolated, unfenced area that can serve as a source for rabbits while requiring fewer management inputs) Continue Rabbit Hemorrhagic Disease Virus (RHDV2) annual vaccinations in both breeding and wild populations When juveniles are available for translocation, prioritize recovery areas that are in the establishing phase In addition, while not analyzed explicitly in the model, discussions during the SDM process led to the identification of the following actions, which the group considered to have potential to benefit the CBPR either directly or indirectly: Increase the amount of suitable habitat available to pygmy rabbits Increase protections for existing and potential recovery areas Design future monitoring to better estimate survival and reproduction, with an emphasis on understanding how these vital rates vary between wild and semi-captive individuals, between vaccinated and unvaccinated individuals, and as a function of habitat factors

BioRxiv↗
USGS2026

Distributions of host heterogeneity in susceptibility show signatures of pathogen geographic structure in an insect baculovirus

Segregated variation between populations is a fundamental evolutionary process leading to parasite specialization, yet the resulting impacts on infection heterogeneity within populations are theoretically and empirically understudied. We asked whether the distribution of host susceptibility to infection within populations carries the signatures of geographic structure from pathogen local adaptation, maladaptation, or generalism in a nuclear polyhedrosis virus that infects the Gulf Fritillary butterfly Dione vanillae . For this virus, there is genetic support for two geographically distinct groups within San Diego County, based on whole genome sequencing of 16 virus isolates. Reciprocal laboratory infections showed evidence of two contrasting viral life history strategies: a ‘generalist’ phenotype that consistently infected variable hosts and a ‘specialist’ that performed slightly better in its local host population. As predicted by our theoretical model, the more consistent infection displayed by the generalist across populations corresponded to lower heterogeneity in susceptibility within populations, modeled as gamma distribution. Furthermore, the generalist phenotype was collected over a wider geographic range despite having a tenfold-lower mean infection rate than the specialist, suggesting that a strategy of more consistent infection provides key fitness advantages across diverse host populations. Intriguingly, when there is variation in host susceptibility, interpretations of pathogen local adaptation are dose-dependent. Measuring infectivity across multiple doses enables estimation of the whole distribution of susceptibility, which provides more reliable identification of pathogen specialization to its local host. Our work demonstrates how trait distributions and not only their mean values can carry quantifiable signatures of eco-evolutionary processes in interspecific interactions.

BioRxiv↗
USGS2001

Unusual bacterioplankton community structure in ultra-oligotrophic Crater Lake

The bacterioplankton assemblage in Crater Lake, Oregon (U.S.A.), is different from communities found in other oxygenated lakes, as demonstrated by four small subunit ribosomal ribonucleic acid (SSU rRNA) gene clone libraries and oligonucleotide probe hybridization to RNA from lake water. Populations in the euphotic zone of this deep (589 m), oligotrophic caldera lake are dominated by two phylogenetic clusters of currently uncultivated bacteria: CL120-10, a newly identified cluster in the verrucomicrobiales, and ACK4 actinomycetes, known as a minor constituent of bacterioplankton in other lakes. Deep-water populations at 300 and 500 m are dominated by a different pair of uncultivated taxa: CL500-11, a novel cluster in the green nonsulfur bacteria, and group I marine crenarchaeota. b-Proteobacteria, dominant in most other freshwater environments, are relatively rare in Crater Lake (<=16% of nonchloroplast bacterial rRNA at all depths). Other taxa identified in Crater Lake libraries include a newly identified candidate bacterial division, ABY1, and a newly identified subcluster, CL0-1, within candidate division OP10. Probe analyses confirmed vertical stratification of several microbial groups, similar to patterns observed in open-ocean systems. Additional similarities between Crater Lake and ocean microbial populations include aphotic zone dominance of group I marine crenarchaeota and green nonsulfur bacteria. Comparison of Crater Lake to other lakes studied by rRNA methods suggests that selective factors structuring Crater Lake bacterioplankton populations may include low concentrations of available trace metals and dissolved organic matter, chemistry of infiltrating hydrothermal waters, and irradiation by high levels of ultraviolet light.

Limnology and Oceanography↗