Patterns of fish deformities and their association with trematode cysts in the Willamette River,Oregon

Synopsis We described skeletal deformities in Willamette River fishes from larval and juvenile specimens collected in 2002 and 2003. Deformities were found in most taxa examined but were more frequent in native broadcast spawners, especially minnows and suckers, than in native or exotic nest builders. Caudal deformities were uniformly distributed throughout the river, but precaudal deformities were more localized near the towns of Newberg and Salem (Wheatland Ferry). In northern pikeminnow, Ptychocheilus oregonensis, deformities were dependent on relative hatch date, with early season fish having about three times the deformity load as late season fish. In a subsample of northern pikeminnow and chiselmouth, Acrocheilus alutaceus, number of deformities was directly related to number of trematode metacercariae and precaudal deformities were twice as likely as caudal deformities to be associated with metacercariae. Based on a logistic regression, the probability of a precaudal deformity was dependent on number of metacercariae and geographic area with the area effect disappearing as the number of cysts increased. A separate analysis showed that some types of deformities were unlikely to be associated with metacercariae. However, even in cases where metacercariae were unlikely to be associated with deformities, metacercariae were usually present elsewhere in the fish and an indirect effect could not be dismissed. The taxonomic, spatial and temporal patterns of skeletal deformities in Willamette River fishes may be due to differences in intermediate host (snail or fish) resistance or susceptibility to parasites, to differences in life history ecology, or to anthropogenic effects that are manifest in increased precaudal deformities near Newberg and Wheatland Ferry or decreased rates elsewhere.     

Effects of Succession on Nitrogen Export in the West-Central Cascades, Oregon

This study examined impacts of succession on N export from 20 headwater stream systems in the west central Cascades of Oregon, a region of low anthropogenic N inputs. The seasonal and successional patterns of nitrate (NO₃−N) concentrations drove differences in total dissolved N concentrations because ammonium (NH₄−N) concentrations were very low (usually < 0.005 mg L⁻¹) and mean dissolved organic nitrogen (DON) concentrations were less variable than nitrate concentrations. In contrast to studies suggesting that DON levels strongly dominate in pristine watersheds, DON accounted for 24, 52, and 51% of the overall mean TDN concentration of our young (defined as predominantly in stand initiation and stem exclusion phases), middle-aged (defined as mixes of mostly understory reinitiation and older phases) and old-growth watersheds, respectively. Although other studies of cutting in unpolluted forests have suggested a harvest effect lasting 5 years or less, our young successional watersheds that were all older than 10 years still lost significantly more N, primarily as NO₃−N, than did watersheds containing more mature forests, even though all forest floor and mineral soil C:N ratios were well above levels reported in the literature for leaching of dissolved inorganic nitrogen. The influence of alder may contribute to these patterns, although hardwood cover was quite low in all watersheds; it is possible that in forested ecosystems with very low anthropogenic N inputs, even very low alder cover in riparian zones can cause elevated N exports. Only the youngest watersheds, with the highest nitrate losses, exhibited seasonal patterns of increased summer uptake by vegetation as well as flushing at the onset of fall freshets. Older watersheds with lower N losses did not exhibit seasonal patterns for any N species. The results, taken together, suggest a role for both vegetation and hydrology in N retention and loss, and add to our understanding of N cycling by successional forest ecosystems influenced by disturbance at various spatial and temporal scales in a region of relatively low anthropogenic N input.     

Organic Nitrogen Retention in the Atchafalaya River Swamp

Freshwater diversions from the lower Mississippi River into the region’s wetlands have been considered an alternative means for reducing nitrogen loading. The Atchafalaya River Swamp, the largest freshwater swamp in North America, carries the entire discharge of the Red River and 30% of the discharge of the Mississippi River, but it is largely unknown how much nitrogen actually can be retained from the overflowing waters of the Mississippi–Atchafalaya River system. Nitrogen discharge from the upper Mississippi River Basin has been implicated as the major cause for the hypoxia in the Northern Gulf of Mexico, which threatens not only the aquatic ecosystem health, but also Louisiana’s fishery industry, among other problems. This study was conducted to determine the change in organic nitrogen mass as water flows through the Atchafalaya River Swamp and into the Gulf of Mexico. By utilizing the river’s long-term discharge and water quality data (1978–2002), monthly and annual organic nitrogen fluxes were quantified, and their relationships with the basin’s hydrologic conditions were investigated. A total Kjeldahl nitrogen (TKN) mass input–output balance between the upstream (Simmesport) and downstream (Morgan City and Wax Lake Outlet) locations was established to examine the organic nitrogen removal potential for this large swamp. The results showed that on average, TKN input into the Atchafalaya was 200 323 tons year⁻¹ and TKN output leaving the basin was 145 917 tons year⁻¹, resulting in a 27% removal rate of organic nitrogen. Monthly TKN input and output in the basin were highest from March to June (input vs. output: 25 000 vs. 18 000 tons month⁻¹) and lowest from August to November (8000 vs. 6000 tons month⁻¹). There was a large variation in both annual and inter-annual organic nitrogen removals. The variability was positively correlated with the amount of inflow water at Simmesport, suggesting that regulating the river’s inflow at the Old River flood control structures may help reduce nitrogen loading of the Mississippi River to the Gulf of Mexico. Furthermore, the in-stream loss of organic nitrogen indicates that previous studies may have overestimated nitrogen discharge from the Mississippi–Atchafalaya River system.     

Riverine Landscape Patch Heterogeneity Drives Riparian Ant Assemblages in the Scioto River Basin,USA

Although the principles of landscape ecology are increasingly extended to include riverine landscapes, explicit applications are few. We investigated associations between patch heterogeneity and riparian ant assemblages at 12 riverine landscapes of the Scioto River, Ohio, USA, that represent urban/developed, agricultural, and mixed (primarily forested, but also wetland, grassland/fallow, and exurban) land-use settings. Using remotely-sensed and ground-collected data, we delineated riverine landscape patch types (crop, grass/herbaceous, gravel, lawn, mudflat, open water, shrub, swamp, and woody vegetation), computed patch metrics (area, density, edge, richness, and shape), and conducted coordinated sampling of surface-active Formicidae assemblages. Ant density and species richness was lower in agricultural riverine landscapes than at mixed or developed reaches (measured using S [total number of species], but not using Menhinick’s Index [D_M]), whereas ant diversity (using the Berger-Park Index [D_BP]) was highest in agricultural reaches. We found no differences in ant density, richness, or diversity among internal riverine landscape patches. However, certain characteristics of patches influenced ant communities. Patch shape and density were significant predictors of richness (S: R² = 0.72; D_M: R²=0.57). Patch area, edge, and shape emerged as important predictors of D_BP (R² = 0.62) whereas patch area, edge, and density were strongly related to ant density (R² = 0.65). Non-metric multidimensional scaling and analysis of similarities distinguished ant assemblage composition in grass and swamp patches from crop, gravel, lawn, and shrub as well as ant assemblages in woody vegetation patches from crop, lawn, and gravel (stress = 0.18, R² = 0.64). These findings lend insight into the utility of landscape ecology to river science by providing evidence that spatial habitat patterns within riverine landscapes can influence assemblage characteristics of riparian arthropods.     

Detection of Cryptococcus gattii in Selected Urban Parks of the Willamette Valley, Oregon

Human and animal infections of the fungus Cryptococcus gattii have been recognized in Oregon since 2006. Transmission is primarily via airborne environmental spores and now thought to be locally acquired due to infection in non-migratory animals and humans with no travel history. Previous published efforts to detect C. gattii from tree swabs and soil samples in Oregon have been unsuccessful. This study was conducted to determine the presence of C. gattii in selected urban parks of Oregon cities within the Willamette Valley where both human and animal cases of C. gattii have been diagnosed. Urban parks were sampled due to spatial and temporal overlap of humans, companion animals and wildlife. Two of 64 parks had positive samples for C. gattii. One park had a positive tree and the other park, 60 miles away, had positive bark mulch samples from a walkway. Genotypic subtypes identified included C. gattii VGIIa and VGIIc, both considered highly virulent in murine host models.     

Climate Change Impacts on Streamflow and Subbasin-Scale Hydrology in the Upper Colorado River Basin

In the Upper Colorado River Basin (UCRB), the principal source of water in the southwestern U.S., demand exceeds supply in most years, and will likely continue to rise. While General Circulation Models (GCMs) project surface temperature warming by 3.5 to 5.6°C for the area, precipitation projections are variable, with no wetter or drier consensus. We assess the impacts of projected 21^st century climatic changes on subbasins in the UCRB using the Soil and Water Assessment Tool, for all hydrologic components (snowmelt, evapotranspiration, surface runoff, subsurface runoff, and streamflow), and for 16 GCMs under the A2 emission scenario. Over the GCM ensemble, our simulations project median Spring streamflow declines of 36% by the end of the 21^st century, with increases more likely at higher elevations, and an overall range of −100 to +68%. Additionally, our results indicated Summer streamflow declines with median decreases of 46%, and an overall range of −100 to +22%. Analysis of hydrologic components indicates large spatial and temporal changes throughout the UCRB, with large snowmelt declines and temporal shifts in most hydrologic components. Warmer temperatures increase average annual evapotranspiration by ∼23%, with shifting seasonal soil moisture availability driving these increases in late Winter and early Spring. For the high-elevation water-generating regions, modest precipitation decreases result in an even greater water yield decrease with less available snowmelt. Precipitation increases with modest warming do not translate into the same magnitude of water-yield increases due to slight decreases in snowmelt and increases in evapotranspiration. For these basins, whether modest warming is associated with precipitation decreases or increases, continued rising temperatures may make drier futures. Subsequently, many subbasins are projected to turn from semi-arid to arid conditions by the 2080 s. In conclusion, water availability in the UCRB could significantly decline with adverse consequences for water supplies, agriculture, and ecosystem health.     

Population genetics of introduced bullfrogs, Rana (Lithobates) catesbeianus, in the Willamette Valley, Oregon, USA

The American bullfrog, Rana (Lithobates) catesbeianus, is endemic to eastern North America, but has been introduced to approximately 40 countries on four continents and is considered one of the hundred worst invasive alien species in the world. Here, we investigated the genetics of invasive bullfrogs in the Willamette Valley, Oregon, USA, where bullfrogs are widespread and abundant to determine: (1) the minimum number of bullfrog introductions; (2) the native source population(s); and (3) whether genetic variation is reduced compared to source populations. To answer these questions, we analyzed partial sequences of the mitochondrial cytochrome b gene for 251 bullfrogs from the Willamette Valley and the native range. We found that bullfrogs from the Mississippi River basin and Great Lakes region were introduced at least once to the Willamette Valley. Genetic variation measured as haplotype diversity (h) and nucleotide diversity (?? _n ) was not significantly different between Willamette Valley and source populations. Our results were in contrast to a recent genetic analysis of invasive bullfrog populations in Europe, which found that genetic variation in European bullfrog populations was much lower than in source populations. European bullfrogs also originated from different source populations than Willamette Valley bullfrogs. The difference in genetic composition between Willamette Valley and European bullfrogs is likely due to differences in their invasion histories and may have implications for the potential of bullfrogs in these different regions to adapt and expand.     

Landsat-based monitoring of annual wetland change in the Willamette Valley of Oregon,USA from 1972 to 2012

In Oregon’s Willamette Valley, remaining wetlands are at high risk to loss and degradation from agricultural activity and urbanization. With an increased need for fine temporal-scale monitoring of sensitive wetlands, we used annual Landsat MSS and TM/ETM+ images from 1972 to 2012 to manually interpret loss, gain, and type conversion of wetland area in the floodplain of the Willamette River. By creating Tasseled Cap Brightness, Greenness, and Wetness indices for MSS data that visually match TM/ETM+ Tasseled Cap images, we were able to construct a complete and consistent, annual time series and utilize the entire Landsat archive. With an extended time series we were also able to compare annual trends of net change in wetland area before and after the no-net-loss policy established under Section 404 of the Clean Water Act in 1990 using a Theil-Sen Slope estimate analysis. Vegetated wetlands experienced a 314 ha net loss of wetland area and non-vegetated wetlands experienced a 393 ha net gain, indicating higher functioning wetlands were replaced in area by non-vegetated wetland habitats such as agricultural and quarry ponds. The majority of both gain and loss in the study area was attributed to gains and losses of agricultural land. After 1990 policy implementations, the rate of wetland area lost slowed for some wetland categories and reversed into trends of gain in wetland area for others, perhaps representative of the success of increased regulations. Overall accuracy of land use classification through manual interpretation was at 80 %. This accuracy increased to 91.1 % when land use classes were aggregated to either wetland or upland categories, indicating that our methodology was more accurate at distinguishing between general upland and wetland than finer categorical classes.     

Nitrogen Retention, Removal, and Saturation in Lotic Ecosystems

Increased nitrogen (N) loading to lotic ecosystems may cause fundamental changes in the ability of streams and rivers to retain or remove N due to the potential for N saturation. Lotic ecosystems will saturate with sustained increases in the N load, but it is unclear at what point saturation will occur. Rates of N transformation in lotic ecosystems will vary depending on the total N load and whether it is an acute or chronic N load. Nitrogen saturation may not occur with only pulsed or short-term increases in N. Overall, saturation of microbial uptake will occur prior to saturation of denitrification of N and denitrification will become saturated prior to nitrification, exacerbating increases in nitrate concentrations and in N export downstream. The rate of N export to downstream ecosystems will increase proportionally to the N load once saturation occurs. Long term data sets showed that smaller lotic ecosystems have a greater capacity to remove in-stream N loads, relative to larger systems. Thus, denitrification is likely to become less important as a N loss mechanism as the stream size increases. There is a great need for long-term studies of N additions in lotic ecosystems and clear distinctions need to be made between ecosystem responses to short-term or periodic increases in N loading and alterations in ecosystem functions due to chronic N loading.     

Nitrogen fixation and denitrification in plankton and periphyton of the Kama River Basin watercourses

The results of studies on molecular nitrogen fixation and denitrification by plankton, epiphytone, and epilithone in a number of natural and anthropogenic waterways of the Kama River Basin are presented for summer and autumn periods of 2005. The nitrogen fixation and denitrification was quantified by acetylene gas chromatography. The phototrophic anoxybiotic purple non-sulfurous bacteria, in particular, of Rhodopseudomonas, Rhodobacter and Rhodocyclus genera, play a significant role in active denitrification in the presence of sulfide-free flow water in the Kama River and its inflows in epilithone, algal-bacterial mats, and biological sewage disposal plants in Perm. On the other hand, the heterocyst cyanobacteria of Anabaena and Aphanizomenon genera had a leading position in active N₂ fixation in the plankton and periphyton of the lower river streams.     

1200 years of fire and vegetation history in the Willamette Valley, Oregon and Washington, reconstructed using high-resolution macroscopic charcoal and pollen analysis

High-resolution macroscopic charcoal and pollen analyses were used to reconstruct the fire and vegetation history of the Willamette Valley for the last 1200 years. Presented in this paper are three new paleoecological reconstructions from Lake Oswego, Porter Lake, and Warner Lake, Oregon, and portions of previous reconstructions from Battle Ground Lake, Washington, and Beaver Lake, Oregon. The reconstructions show that prior to Euro-American settlement vegetation and fire regimes were influenced by a combination of natural and anthropogenic factors. Battle Ground Lake shows a stronger influence from climate, while Lake Oswego, Beaver Lake, Porter Lake, and Warner Lake were more controlled by human activity. However, human-set fires were also modulated by regional climate variability during the Medieval Climate Anomaly and the Little Ice Age. Fire reconstructions from Battle Ground Lake, Lake Oswego, Beaver Lake, and Porter Lake imply that fires were infrequent in the Willamette Valley 200-300 years prior to Euro-American settlement. The decline of Native American populations due to introduced disease may have led to this reduction in fire activity. The prehistoric record from Warner Lake, however, indicates that fires in the foothills of the Cascade Range were more frequent than on the valley floor, at least until ca. AD 1800. The historic portions of the reconstructions indicate that Euro-American land clearance for agriculture and logging produced the most dramatic shifts in vegetation and fire regimes. All five records indicate that few fires in the Willamette Valley have occurred since ca. AD 1930, and fires today are predominantly grass fires.     

Seasonal variations in growth, condition and gonads of Dormitator latifrons (Richardson) in the Chone River Basin, Ecuador

Growth in length, condition, and gonads of a food fish, Dormitator latifrons , were studied in the Chone River basin, Ecuador, in 1981. The river was bordered by floodplains in the upstream freshwater zone, and by mangrove swamps and shrimp farms in the downstream estuarine zone. The climate was marked by wet (January to April) and dry (May to December) seasons. During the dry season, an earth dam in the river prevented movement of water and fish between upstream and downstream zones. At the end of the dry season, most of the upstream floodplains were dry, and the main fish refuges were in downstream areas in deep pools in the river upstream. During the floods, fish migrated from downstream areas towards upstream floodplains. Growth rates and condition increased when water levels were high or salinity was low and decreased when water levels were low or salinity was high. Seasonal changes in gonads and abundance of juveniles indicated that reproduction occurred during the floods, but there was some reproduction in the dry season. Reproduction occurred in upstream and downstream zones and appeared to be stimulated by a complex of factors, including water levels, currents and salinity. The yield in flood plain sites was estimated as c. 115 kg ha⁻¹ in 1981.     

Pre-spawning migration of adult Pacific lamprey, <Emphasis Type="BoldItalic">Entosphenus tridentatus</Emphasis>, in the Willamette River,Oregon, U.S.A.

We describe the migration distances and timing of the adult Pacific lamprey, Entosphenus tridentatus, in the Willamette River Basin (Oregon, U.S.A.). We conducted aerial surveys to track radio-tagged fish upstream of a major waterfall and hydropower complex en route to spawning areas. We detected 24 out of the 43 fish that passed the waterfall-hydropower complex. Of the detected fish, 17 were detected multiple times. Their maximum migration distance upstream in the mainstem Willamette approximated a normal distribution. The maximum distance migrated upstream did not significantly correlate with total body length (r = −0.186, P = 0.385) or date that the fish passed Willamette Falls (r = −0.118, P = 0.582). Fish migrated primarily during the spring to early summer period before stopping during the summer, when peak river temperatures (≥20°C). However, at least three fish continued to migrate upstream after September. Behavior ranged from relatively slow migration, followed by holding; to rapid migration, followed by slow migration further up in the basin. This study provides a basis for informing more detailed research on Pacific lamprey in the future.     

Coupled Nitrogen and Calcium Cycles in Forests of the Oregon Coast Range

Nitrogen (N) is a critical limiting nutrient that regulates plant productivity and the cycling of other essential elements in forests. We measured foliar and soil nutrients in 22 young Douglas-fir stands in the Oregon Coast Range to examine patterns of nutrient availability across a gradient of N-poor to N-rich soils. N in surface mineral soil ranged from 0.15 to 1.05% N, and was positively related to a doubling of foliar N across sites. Foliar N in half of the sites exceeded 1.4% N, which is considered above the threshold of N-limitation in coastal Oregon Douglas-fir. Available nitrate increased five-fold across this gradient, whereas exchangeable magnesium (Mg) and calcium (Ca) in soils declined, suggesting that nitrate leaching influences base cation availability more than soil parent material across our sites. Natural abundance strontium isotopes (⁸⁷Sr/⁸⁶Sr) of a single site indicated that 97% of available base cations can originate from atmospheric inputs of marine aerosols, with negligible contributions from weathering. Low annual inputs of Ca relative to Douglas-fir growth requirements may explain why foliar Ca concentrations are highly sensitive to variations in soil Ca across our sites. Natural abundance calcium isotopes (δ⁴⁴Ca) in exchangeable and acid leachable pools of surface soil measured at a single site showed 1 per mil depletion relative to deep soil, suggesting strong Ca recycling to meet tree demands. Overall, the biogeochemical response of these Douglas-fir forests to gradients in soil N is similar to changes associated with chronic N deposition in more polluted temperate regions, and raises the possibility that Ca may be deficient on excessively N-rich sites. We conclude that wide gradients in soil N can drive non-linear changes in base-cation biogeochemistry, particularly as forests cross a threshold from N-limitation to N-saturation. The most acute changes may occur in forests where base cations are derived principally from atmospheric inputs.     

Seasonal and Habitat Influences on Fish Communities within the Lower Yasuni River Basin of the Ecuadorian Amazon

We sampled lagoon, river and forest stream habitats during the rising water, wet, falling water, and dry seasons in the lowland region of the Yasuni National Reserve in the Ecuadorian Amazon. We collected 195 species, increasing the current number of species for the Napo River basin to approximately 562. The steady rate of species accumulation per sample suggests that the fish fauna is still undersampled. Lagoon, river and forest stream fish communities are highly diverse and variable, composed of common species found within several habitats, of characteristic species found throughout the year, and of seasonally migrating species. Characteristic lagoon species were mainly the curimatids Curimata vittata, Psectrogaster amazonica, Potamorhina altamazonica, P. latior and Cyphocharax plumbeus. The characins Hyphessobrycon copelandi and Hemigrammus cf. lunatus and the catfishes Nemadoras humeralis, Pimelodella sp. C and Sorubim sp. A were characteristic river species. Characteristic forest stream species included Hoplias malabaricus, Hyphessobrycon copelandi, Pimelodella sp. B and Sternopyugus macrurus. During the dry season, lagoon and river habitats had the highest number of individuals and species, as fishes were concentrated in decreasing habitat area. In contrast, stream habitats had the highest species richness and abundance during the rising water and falling water seasons. Species collected included vital food fishes and seasonal migrants. The migratory catfishes Brachyplatystoma vaillantii, Hemisorubim platyrhynchos, Platynematichthys notatus, Platystomatichthys sturio and Sorubim lima were collected during the falling water season, which suggests that these species may begin migrating earlier than expected. These findings highlight the importance of seasonality for both adequately assessing aquatic biodiversity and for developing research and conservation programs encompassing whole river ecosystems.     

Seasonal Prevalence of Enteropathogenic Vibrio and Their Phages in the Riverine Estuarine Ecosystem of South Bengal

Diarrheal disease remains an unsolved problem in developing countries. The emergence of new etiological agents (non-cholera vibrios) is a major cause of concern for health planners. We attempted to unveil the seasonal dynamics of entero-pathogenic Vibrios in Gangetic riverine-estuarine ecosystem. 120 surface water samples were collected for a period of one year from 3 sampling sites on the Hooghly river. Five enteropathogenic Vibrio species, V. cholerae (35%), V. parahaemolyticus (22.5%), V. mimicus (19.1%), V. alginolyticus (15.8%) and V. vulnificus (11.6%), were present in the water samples. The vibriophages, V. vulnificus ɸ (17.5%), V. alginolyticus ɸ (17.5%), V. parahaemolyticus ɸ (10%), V. cholerae non-O1/O139 ɸ (26.6%) and V. mimicus ɸ (9.1%), were also detected in these samples. The highest number of Vibrios were noted in the monsoon (20–34°C), and to a lesser extent, in the summer (24–36°C) seasons. Samples positive for phages for any of the identified Vibrio species were mostly devoid of that particular bacterial organism and vice versa. The detection of toxin genes and resistance to β-lactam antibiotics in some environmental enteropathogenic Vibrio species in the aquatic niches is a significant outcome. This finding is instrumental in the south Bengal diarrhoeal incidence.     

Soil Homogenization Modifies Productivity,Nitrogen Retention and Decomposition in Restored Grassland

Ecosystems - At the local (within site) scale, soil heterogeneity can influence ecosystem function. However, in former agricultural systems, soil heterogeneity can be low as a legacy of tillage...     

Seasonal and interannual variability in the taxonomic composition and production dynamics of phytoplankton assemblages in 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.