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Disentangling the environmental and spatial drivers of biological communities across large scales increasingly challenges modern ecology in a rapidly changing world. Here, we investigate the hierarchical and trait‐based organization of regional and local factors of zooplankton communities at a macroscale of 1240 mountain lakes and ponds spanning western North America (California, USA, to Yukon Territory, Canada). Variation partitioning was used to test the hypothesized importance of climate, connectivity, catchment features, and exotic sportfish to zooplankton beta‐diversity in the context of key functional traits (body size and reproductive dispersal potential) given the pronounced environmental heterogeneity (e.g. thermal gradients), topographic barriers, and legacy of stocked fish in mountainous regions. Dispersal limitation was inferred from multispecies patch connectivity estimates based on nearest and average distances to occupied patches. Environmental heterogeneity best explained community composition as catchment/lake features (morphometry, land cover, and lithology) collectively captured greater variation than did climate (temperature, precipitation, and solar radiation), local stocking, or connectivity; however, single climatic variables captured the most variation individually. Macrospatial variation by larger obligate sexual species was better explained than that by smaller cyclically parthenogenetic asexual species. Our results provide several novel insights into the macroecology of zooplankton of the North American Cordillera, demonstrating their stronger associations to climatically driven aquatic‐terrestrial habitat coupling than dynamics arising from introduced salmonids, human land‐use, or species dispersal. These findings highlight the clear and important role of these communities as bioindicators of the limnological impacts of accelerating rates of climate change, as their responses appear relatively not confounded by local human perturbations or dispersal limitation.

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. β-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.

During the period 1996–2003, a population of introduced Salvelinus fontinalis was eradicated from a montane lake in Mount Rainier National Park, Washington State, USA. Using mostly gill-nets, 2185 fish were removed. Snorkel and visual encounter surveys (n = 10 and 6, respectively) were completed 1996–2001, to document the apparent abundances of amphibian species present in the lake and an adjacent shallow pond during fish presence and removal. During this period only 7 Ambystoma gracile larvae and 6 Rana cascadae adults were observed in the lake; no amphibians were observed in the pond. After fish removal, lake snorkel and visual encounter surveys (n = 9 and 10, respectively) conducted between 2004 and 2015 collectively documented the apparent increase in abundances of A. gracilie (n = 398), A. macrodactylum (n = 68), Ambystoma spp. (n = 184), Rana cascadae (n = 357), and Ascaphus truei (n = 12). Pond visual encounter surveys conducted between 2005 and 2012 documented the increased presence of Ambystoma spp. (n = 110) and Rana cascadae (n = approximately 5600+) larvae. Although the number of amphibian species detected and their apparent abundances varied among surveys and years, the abundances of the amphibian species in Hidden Lake increased markedly after removal of the introduced fish population.

Issue Title: Theme: Long-term Limnological Research and Monitoring at Crater Lake, Oregon The distribution of bacterial and archaeal species in Crater Lake plankton varies dramatically over depth and with time, as assessed by hybridization of group-specific oligonucleotides to RNA extracted from lakewater. Nonmetric, multidimensional scaling (MDS) analysis of relative bacterial phylotype densities revealed complex relationships among assemblages sampled from depth profiles in July, August and September of 1997 through 1999. CL500-11 green nonsulfur bacteria (Phylum Chloroflexi) and marine Group I crenarchaeota are consistently dominant groups in the oxygenated deep waters at 300 and 500 m. Other phylotypes found in the deep waters are similar to surface and mid-depth populations and vary with time. Euphotic zone assemblages are dominated either by β-proteobacteria or CL120-10 verrucomicrobia, and ACK4 actinomycetes. MDS analyses of euphotic zone populations in relation to environmental variables and phytoplankton and zooplankton population structures reveal apparent links between Daphnia pulicaria zooplankton population densities and microbial community structure. These patterns may reflect food web interactions that link kokanee salmon population densities to community structure of the bacterioplankton, via fish predation on Daphnia with cascading consequences to Daphnia bacterivory and predation on bacterivorous protists. These results demonstrate a stable bottom-water microbial community. They also extend previous observations of food web-driven changes in euphotic zone bacterioplankton community structure to an oligotrophic setting.[PUBLICATION ABSTRACT]

Issue Title: Theme: Long-term Limnological Research and Monitoring at Crater Lake, Oregon Taxonomic composition and production dynamics of phytoplankton assemblages in Crater Lake, Oregon, were examined during time periods between 1984 and 2000. The objectives of the study were (1) to investigate spatial and temporal patterns in species composition, chlorophyll concentration, and primary productivity relative to seasonal patterns of water circulation; (2) to explore relationships between water column chemistry and the taxonomic composition of the phytoplankton; and (3) to determine effects of primary and secondary consumers on the phytoplankton assemblage. An analysis of 690 samples obtained on 50 sampling dates from 14 depths in the water column found a total of 163 phytoplankton taxa, 134 of which were identified to genus and 101 were identified to the species or variety level of classification. Dominant species by density or biovolume included Nitzschia gracilis, Stephanodiscus hantzschii, Ankistrodesmus spiralis, Mougeotia parvula, Dinobryon sertularia, Tribonema affine, Aphanocapsa delicatissima, Synechocystis sp., Gymnodinium inversum, and Peridinium inconspicuum. When the lake was thermally stratified in late summer, some of these species exhibited a stratified vertical distribution in the water column. A cluster analysis of these data also revealed a vertical stratification of the flora from the middle of the summer through the early fall. Multivariate test statistics indicated that there was a significant relationship between the species composition of the phytoplankton and a corresponding set of chemical variables measured for samples from the water column. In this case, concentrations of total phosphorus, ammonia, total Kjeldahl nitrogen, and alkalinity were associated with interannual changes in the flora; whereas pH and concentrations of dissolved oxygen, orthophosphate, nitrate, and silicon were more closely related to spatial variation and thermal stratification. The maximum chlorophyll concentration when the lake was thermally stratified in August and September was usually between depths of 100 m and 120 m. In comparison, the depth of maximum primary production ranged from 60 m to 80 m at this time of year. Regression analysis detected a weak negative relationship between chlorophyll concentration and Secchi disk depth, a measure of lake transparency. However, interannual changes in chlorophyll concentration and the species composition of the phytoplankton could not be explained by the removal of the septic field near Rim Village or by patterns of upwelling from the deep lake. An alternative trophic hypothesis proposes that the productivity of Crater Lake is controlled primarily by long-term patterns of climatic change that regulate the supply of allochthonous nutrients.[PUBLICATION ABSTRACT]

Issue Title: Theme: Long-term Limnological Research and Monitoring at Crater Lake, Oregon Crater Lake is located in the caldera of Mount Mazama in Crater Lake National Park, Oregon. The lake has a surface area of about 53 km^sup 2^at an elevation of 1882 m and a maximum depth of 594 m. Limited studies of this ultraoligotrophic lake conducted between 1896 and 1981, lead to a 10-year limnological study to evaluate any potential degradation of water quality. No long-term variations in water quality were observed that could be attributed to anthropogenic activity. Building on the success of this study, a permanent limnological program has been established with a long-term monitoring program to insure a reliable data base for use in the future. Of equal importance, this program serves as a research platform to develop and communicate to the public a better understanding of the coupled biological, physical, and geochemical processes in the lake and its surrounding environment. This special volume represents our current state of knowledge of the status of this pristine ecosystem including its special optical properties, algal nutrient limitations, pelagic bacteria, and models of the inter-relationships of thermal properties, nutrients, phytoplankton, deep-water mixing, and water budgets.[PUBLICATION ABSTRACT]

Issue Title: Theme: Long-term Limnological Research and Monitoring at Crater Lake, Oregon Crater Lake is a unique environment to evaluate the ecology of introduced kokanee and rainbow trout because of its otherwise pristine state, low productivity, absence of manipulative management, and lack of lotic systems for fish spawning. Between 1986 and 2004, kokanee displayed a great deal of variation in population demographics with a pattern that reoccurred in about 10 years. We believe that the reoccurring pattern resulted from density dependent growth, and associated changes in reproduction and abundance, driven by prey resource limitation that resulted from low lake productivity exacerbated by prey consumption when kokanee were abundant. Kokanee fed primarily on small-bodied prey from the mid-water column; whereas rainbow trout fed on large-bodied prey from the benthos and lake surface. Cladoceran zooplankton abundance may be regulated by kokanee. And kokanee growth and reproductive success may be influenced by the availability of Daphnia pulicaria, which was absent in zooplankton samples collected annually from 1990 to 1995, and after 1999. Distribution and diel migration of kokanee varied over the duration of the study and appeared to be most closely associated with prey availability, maximization of bioenergetic efficiency, and fish density. Rainbow trout were less abundant than were kokanee and exhibited less variation in population demographics, distribution, and food habits. There is some evidence that the population dynamics of rainbow trout were in-part related to the availability of kokanee as prey.[PUBLICATION ABSTRACT]

Issue Title: Theme: Long-term Limnological Research and Monitoring at Crater Lake, Oregon Crater Lake covers the floor of the Mount Mazama caldera that formed 7700 years ago. The lake has a surface area of 53 km^sup 2^ and a maximum depth of 594 m. There is no outlet stream and surface inflow is limited to small streams and springs. Owing to its great volume and heat, the lake is not covered by snow and ice in winter unlike other lakes in the Cascade Range. The lake is isothermal in winter except for a slight increase in temperature in the deep lake from hyperadiabatic processes and inflow of hydrothermal fluids. During winter and spring the water column mixes to a depth of about 200-250 m from wind energy and convection. Circulation of the deep lake occurs periodically in winter and spring when cold, near-surface waters sink to the lake bottom; a process that results in the upwelling of nutrients, especially nitrate-N, into the upper strata of the lake. Thermal stratification occurs in late summer and fall. The maximum thickness of the epilimnion is about 20 m and the metalimnion extends to a depth of about 100 m. Thus, most of the lake volume is a cold hypolimnion. The year-round near-bottom temperature is about 3.5°C. Overall, hydrothermal fluids define and temporally maintain the basic water quality characteristics of the lake (e.g., pH, alkalinity and conductivity). Total phosphorus and orthophosphate-P concentrations are fairly uniform throughout the water column, where as total Kjeldahl-N and ammonia-N are highest in concentration in the upper lake. Concentrations of nitrate-N increase with depth below 200 m. No long-term changes in water quality have been detected. Secchi disk (20-cm) clarity varied seasonally and annually, but was typically highest in June and lowest in August. During the current study, August Secchi disk clarity readings averaged about 30 m. The maximum individual clarity reading was 41.5 m in June 1997. The lowest reading was 18.1 m in July 1995. From 1896 (white-dinner plate) to 2003, the average August Secchi disk reading was about 30 m. No long-term changes in the Secchi disk clarity were observed. Average turbidity of the water column (2-550 m) between June and September from 1991 to 2000 as measured by a transmissometer ranged between 88.8% and 90.7%. The depth of 1% of the incident solar radiation during thermal stratification varied annually between 80 m and 100 m. Both of these measurements provided additional evidence about the exceptional clarity of Crater Lake.[PUBLICATION ABSTRACT]

Issue Title: Theme: Long-term Limnological Research and Monitoring at Crater Lake, Oregon We addressed potential sources of error in estimating the water clarity of mountain lakes by investigating the use of beam transmissometer measurements to estimate Secchi disk depth. The optical properties Secchi disk depth (SD) and beam transmissometer attenuation (BA) were measured in Crater Lake (Crater Lake National Park, Oregon, USA) at a designated sampling station near the maximum depth of the lake. A standard 20 cm black and white disk was used to measure SD. The transmissometer light source had a nearly monochromatic wavelength of 660 nm and a path length of 25 cm. We created a SD prediction model by regression of the inverse SD of 13 measurements recorded on days when environmental conditions were acceptable for disk deployment with BA averaged over the same depth range as the measured SD. The relationship between inverse SD and averaged BA was significant and the average 95% confidence interval for predicted SD relative to the measured SD was ±1.6 m (range = -4.6 to 5.5 m) or ±5.0%. Eleven additional sample dates tested the accuracy of the predictive model. The average 95% confidence interval for these sample dates was ±0.7 m (range = -3.5 to 3.8 m) or ±2.2%. The 1996-2000 time-series means for measured and predicted SD varied by 0.1 m, and the medians varied by 0.5 m. The time-series mean annual measured and predicted SD's also varied little, with intra-annual differences between measured and predicted mean annual SD ranging from -2.1 to 0.1 m. The results demonstrated that this prediction model reliably estimated Secchi disk depths and can be used to significantly expand optical observations in an environment where the conditions for standardized SD deployments are limited.[PUBLICATION ABSTRACT]

The larval stage of the long-toed salamander (Ambystoma macrodactylum) is the top vertebrate predator in high-elevation fishless lakes in the North Cascades National Park Service Complex, Washington (U.S.A.). Although most of these high-elevation lakes were naturally fishless, trout have been stocked in many of them. We sought to determine the effects of physicochemical factors and introduced trout on abundance and behavior of A. macrodactylum larvae. Larval salamander densities were estimated by snorkeling. Snorkelers carefully searched through substrate materials within 2 m of the shoreline and recorded the number of larvae observed and if larvae were hidden in benthic substrates. Physicochemical factors were measured in each lake on the same day that snorkel surveys were conducted. In fishless lakes, larval salamander densities were positively related to total Kjeldahl-N concentration and negatively related to lake elevation. Crustacean zooplankton, especially cladocerans, were important food resources for larval A. macrodactylum. Crustacean zooplankton and cladoceran densities were positively related to total Kjeldahl-N, suggesting that increased food resources contributed to increased densities of larval A. macrodactylum. Differences in larval salamander densities between fish and fishless lakes were related to total Kjeldahl-N concentrations and the reproductive status of trout. Mean larval salamander densities for fishless lakes with total Kjeldahl-N < 0.045 mg/L were not significantly different from mean larval densities in lakes with reproducing trout or in lakes with nonreproducing trout. In fishless lakes with total Kjeldahl-N ≥ 0.045 mg/L, however, mean larval densities were significantly higher than in lakes with reproducing trout where fish reached high densities. In fishless lakes with total Kjeldahl-N ≥ 0.095 mg/L, mean larval densities were significantly higher than in lakes with nonreproducing trout where trout fry were stocked at low densities. Reduced larval salamander densities in lakes with trout likely resulted from trout predation. There were no significant differences in the percentage of larvae hidden in benthic substrates between fishless lakes and lakes with fish. Our results imply that assessment of the effects of fish on amphibians requires an understanding of natural abiotic and biotic factors and processes influencing amphibian distribution and abundance.