Long‐term zooplankton responses to nutrient and consumer subsidies arising from migratory sockeye salmon (Oncorhynchus nerka)

Migratory animals, such as Pacific salmon, can significantly shape communities in recipient habitats both by altering the flux of resources, and changing community composition and subsequent trophic interactions. Here we mainly used paleoecological records from natural sockeye salmon nursery lakes to quantify the response of plankton communities to the influx of salmon‐derived nutrients and consumers (juvenile salmon). Our long‐term data show that increases in the density of spawning salmon often elevated influx of nutrients, and, in turn, zooplankton production over the past few centuries. In contrast, significant correlations were not detected in two lakes with extremely low or high average spawner densities (i.e. 1.5 and 34.7 × 10³ spawners km^?2 year^?1 respectively). With increasing spawner densities across lakes, analysis of the size structure of subfossils in sediments revealed a strong decrease in body size of a main juvenile salmon prey item (Eubosmina longispina; r²= 0.36, p < 0.001, n = 67), consistent with an overriding effect of predation in lakes with high salmon densities. These long‐term data not only highlight the key role of salmon‐derived nutrients in stimulating plankton communities, but also suggest that the relative effect of nutrient and consumer subsidies varies along gradients of lake production, despite a single ultimate causal mechanism (migrating fish).     

Stable isotope evidence indicates the incorporation into Japanese catchments of marine‐derived nutrients transported by spawning Pacific Salmon

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Lack of parallel genetic patterns underlying the repeated ecological divergence of beach and stream‐spawning kokanee salmon

Recent progress in methods for detecting adaptive population divergence in situ shows promise for elucidating the conditions under which selection acts to generate intraspecific diversity. Rapid ecological diversification is common in fishes; however, the role of phenotypic plasticity and adaptation to local environments is poorly understood. It is now possible to investigate genetic patterns to make inferences regarding phenotypic traits under selection and possible mechanisms underlying ecotype divergence, particularly where similar novel phenotypes have arisen in multiple independent populations. Here, we employed a bottom‐up approach to test for signatures of directional selection associated with divergence of beach‐ and stream‐spawning kokanee, the obligate freshwater form of sockeye salmon (Oncorhynchus nerka). Beach‐ and stream‐spawners co‐exist in many post‐glacial lakes and exhibit distinct reproductive behaviours, life‐history traits and spawning habitat preferences. Replicate ecotype pairs across five lakes in British Columbia, Canada were genotyped at 57 expressed sequence tag‐linked and anonymous microsatellite loci identified in a previous genome scan. Fifteen loci exhibited signatures of directional selection (high F_ST outliers), four of which were identified in multiple lakes. However, the lack of parallel genetic patterns across all lakes may be a result of: 1) an inability to detect loci truly under selection; 2) alternative genetic pathways underlying ecotype divergence in this system; and/or 3) phenotypic plasticity playing a formative role in driving kokanee spawning habitat differences. Gene annotations for detected outliers suggest pathogen resistance and energy metabolism as potential mechanisms contributing to the divergence of beach‐ and stream‐spawning kokanee, but further study is required.     

Carcass analogues provide marine subsidies for macroinvertebrates and juvenile Atlantic salmon in temperate oligotrophic streams

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Genomic signatures of fine‐scale local selection in Atlantic salmon suggest involvement of sexual maturation,energy homeostasis and immune defence‐related genes

Elucidating the genetic basis of adaptation to the local environment can improve our understanding of how the diversity of life has evolved. In this study, we used a dense SNP array to identify candidate loci potentially underlying fine‐scale local adaptation within a large Atlantic salmon (Salmo salar) population. By combining outlier, gene–environment association and haplotype homozygosity analyses, we identified multiple regions of the genome with strong evidence for diversifying selection. Several of these candidate regions had previously been identified in other studies, demonstrating that the same loci could be adaptively important in Atlantic salmon at subdrainage, regional and continental scales. Notably, we identified signals consistent with local selection around genes associated with variation in sexual maturation, energy homeostasis and immune defence. These included the large‐effect age‐at‐maturity gene vgll3, the known obesity gene mc4r, and major histocompatibility complex II. Most strikingly, we confirmed a genomic region on Ssa09 that was extremely differentiated among subpopulations and that is also a candidate for local selection over the global range of Atlantic salmon. This region colocalized with a haplotype strongly associated with spawning ecotype in sockeye salmon (Oncorhynchus nerka), with circumstantial evidence that the same gene (six6) may be the selective target in both cases. The phenotypic effect of this region in Atlantic salmon remains cryptic, although allelic variation is related to upstream catchment area and covaries with timing of the return spawning migration. Our results further inform management of Atlantic salmon and open multiple avenues for future research.     

Inter-annual variation in responses of water chemistry and epilithon to Pacific salmon spawners in an Alaskan stream

1. Pacific salmon (Oncorhynchus spp.) deliver salmon‐derived nutrients (SDN) to the streams in which they spawn. However, many stream parameters, such as discharge and spawner abundance, can vary from year to year, which could alter the quantity and flux of SDN. 2. Over six consecutive years, we studied responses in streamwater chemistry and epilithon (i.e. the microbial community on submerged rocks) to salmon spawners in Fish Creek, southeastern Alaska, U.S.A. The lower reach of Fish Creek receives spawners of several salmon species, while the upper reach does not receive spawners because of an intervening waterfall. 3. We estimated salmon spawner biomass, analysed water chemistry [ammonium, nitrate, soluble reactive phosphorus (SRP) and dissolved organic carbon (DOC)], and measured epilithon abundance [as chlorophyll a (chl a) and ash‐free dry mass (AFDM)] in Fish Creek. Measurements were made in both the upper and lower reaches, before, during and after the major salmon runs. 4. Absolute values and relative differences indicated that the presence of salmon spawners consistently increased dissolved ammonium (by 58 μg L⁻¹ on average, 41× over background), SRP (by 6 μg L⁻¹, 14×), epilithon chl a (by 35 mg m⁻², 16×), and epilithon AFDM (by 3 g m⁻², 8×). Salmon spawners did not increase nitrate or DOC in either absolute or relative amounts. The persistence and magnitude of spawner effects varied among years and appeared to reflect weather‐driven hydrology as well as spawner biomass. 5. Salmon‐derived nutrients can stimulate the growth of primary producers by increasing streamwater nutrient concentrations, but this positive influence may be modulated by other factors, such as water temperature and discharge. To better assess the ecological influence of SDN on stream biota, future studies should explicitly consider the role of key environmental factors and their temporal and spatial dynamics in stream ecosystems.     

Hemispheric‐scale patterns of climate‐related shifts in planktonic diatoms from North American and European lakes

A synthesis of over 200 diatom‐based paleolimnological records from nonacidified/nonenriched lakes reveals remarkably similar taxon‐specific shifts across the Northern Hemisphere since the 19th century. Our data indicate that these diatom shifts occurred in conjunction with changes in freshwater habitat structure and quality, which, in turn, we link to hemispheric warming trends. Significant increases in the relative abundances of planktonic Cyclotella taxa (P<0.01) were concurrent with sharp declines in both heavily silicified Aulacoseira taxa (P<0.01) and benthic Fragilaria taxa (P<0.01). We demonstrate that this trend is not limited to Arctic and alpine environments, but that lakes at temperate latitudes are now showing similar ecological changes. As expected, the onset of biological responses to warming occurred significantly earlier (P<0.05) in climatically sensitive Arctic regions (median age=ad 1870) compared with temperate regions (median age=ad 1970). In a detailed paleolimnological case study, we report strong relationships (P<0.005) between sedimentary diatom data from Whitefish Bay, Lake of the Woods (Ontario, Canada), and long‐term changes in air temperature and ice‐out records. Other potential environmental factors, such as atmospheric nitrogen deposition, could not explain our observations. These data provide clear evidence that unparalleled warming over the last few decades resulted in substantial increases in the length of the ice‐free period that, similar to 19th century changes in high‐latitude lakes, likely triggered a reorganization of diatom community composition. We show that many nonacidified, nutrient‐poor, freshwater ecosystems throughout the Northern Hemisphere have crossed important climatically induced ecological thresholds. These findings are worrisome, as the ecological changes that we report at both mid‐ and high‐latitude sites have occurred with increases in mean annual air temperature that are less than half of what is projected for these regions over the next half century.     

Stream food web response to a salmon carcass analogue addition in two central Idaho, U.S.A. streams

1. Pacific salmon and steelhead once contributed large amounts of marine‐derived carbon, nitrogen and phosphorus to freshwater ecosystems in the Pacific Northwest of the United States of America (California, Oregon, Washington and Idaho). Declines in historically abundant anadromous salmonid populations represent a significant loss of returning nutrients across a large spatial scale. Recently, a manufactured salmon carcass analogue was developed and tested as a safe and effective method of delivering nutrients to freshwater and linked riparian ecosystems where marine‐derived nutrients have been reduced or eliminated. 2. We compared four streams: two reference and two treatment streams using salmon carcass analogue(s) (SCA) as a treatment. Response variables measured included: surface streamwater chemistry; nutrient limitation status; carbon and nitrogen stable isotopes; periphyton chlorophyll a and ash‐free dry mass (AFDM); macroinvertebrate density and biomass; and leaf litter decomposition rates. Within each stream, upstream reference and downstream treatment reaches were sampled 1 year before, during, and 1 year after the addition of SCA. 3. Periphyton chlorophyll a and AFDM and macroinvertebrate biomass were significantly higher in stream reaches treated with SCA. Enriched stable isotope (δ¹⁵N) signatures were observed in periphyton and macroinvertebrate samples collected from treatment reaches in both treatment streams, indicating trophic transfer from SCA to consumers. Densities of Ephemerellidae, Elmidae and Brachycentridae were significantly higher in treatment reaches. Macroinvertebrate community composition and structure, as measured by taxonomic richness and diversity, did not appear to respond significantly to SCA treatment. Leaf breakdown rates were variable among treatment streams: significantly higher in one stream treatment reach but not the other. Salmon carcass analogue treatments had no detectable effect on measured water chemistry variables. 4. Our results suggest that SCA addition successfully increased periphyton and macroinvertebrate biomass with no detectable response in streamwater nutrient concentrations. Correspondingly, no change in nutrient limitation status was detected based on dissolved inorganic nitrogen to soluble reactive phosphorus ratios (DIN/SRP) and nutrient‐diffusing substrata experiments. Salmon carcass analogues appear to increase freshwater productivity. 5. Salmon carcass analogues represent a pathogen‐free nutrient enhancement tool that mimics natural trophic transfer pathways, can be manufactured using recycled fish products, and is easily transported; however, salmon carcass analogues should not be viewed as a replacement for naturally spawning salmon and the important ecological processes they provide.     

Responses of microbial phototrophs to late‐Holocene environmental forcing of lakes in south‐west Greenland

1. The biological structure of arctic lakes is changing rapidly, apparently in response to global change processes such as increasing air temperatures, although altered nutrient stoichiometry may also be an important driver. Equally important, however, are local factors (e.g. landscape setting, hydrological linkages and trophic interactions) that may mediate responses of individual lakes at the regional scale. Despite general acknowledgement of the importance of local factors, there has been little focus on among‐lake variability in the response to environmental change. 2. Sedimentary pigments, organic carbon and nitrogen, and biogenic silica (BSi) in ²¹⁰Pb and ¹⁴C‐dated sediment cores from three contrasting lakes in the Kangerlussuaq area (c. 67°N, 51°W) of south‐west Greenland were used to reconstruct algal and phototrophic bacterial ecological change during the late‐Holocene. Water chemistry for the individual lakes varies in terms of conductivity (range: 30–3000 μS cm^?1) and stratification regimes (cold monomictic, dimictic and meromictic), linked with their position along the regional climate gradient from the coast and to the present ice sheet margin. 3. Despite essentially similar regional climate forcing over the last c. 1000 years, marked differences among lake types were observed in the phototrophic communities and their temporal variability. Considerable short‐term variability occurred in an oligosaline, meromictic lake (SS1371), dominated by purple sulphur bacterial pigments, most likely due to a tight coupling between the position of the chemocline and the phototrophic community. Communities in a lake (SS86) located on a nunatak, just beyond the edge of the present ice sheet shifted in a nonlinear pattern, approximately 1000 cal. years BP, possibly due to lake‐level lowering and loss of outflow during the Medieval Climate Anomaly. This regime shift was marked by a substantial expansion of green sulphur bacteria. 4. A dilute, freshwater coastal lake (SS49) dominated by benthic algae was relatively stable until ca. 1900 AD when rates of community change began to increase. These changes in benthic algal pigments are correlated with substantial declines (1.3–0.44‰) in δ¹⁵N that are indicative of increased deposition of atmospheric inputs of industrially derived NOx into the atmosphere. 5. Climate control on lake ecosystem functioning has been assumed to be particularly important in the Arctic. This study, however, illustrates a complex spatial response to climate forcing at the regional scale and emphasises differences in the relative importance of changes in the mass (m, both precipitation and nutrients) and energy flux (E) to lakes for the phototrophic community structure of low‐arctic Greenland lakes.     

Resurrecting an extinct salmon evolutionarily significant unit: archived scales, historical DNA and implications for restoration

Archival scales from 603 sockeye salmon (Oncorhynchus nerka), sampled from May to July 1924 in the lower Columbia River, were analysed for genetic variability at 12 microsatellite loci and compared to 17 present‐day O. nerka populations—exhibiting either anadromous (sockeye salmon) or nonanadromous (kokanee) life histories—from throughout the Columbia River Basin, including areas upstream of impassable dams built subsequent to 1924. Statistical analyses identified four major genetic assemblages of sockeye salmon in the 1924 samples. Two of these putative historical groupings were found to be genetically similar to extant evolutionarily significant units (ESUs) in the Okanogan and Wenatchee Rivers (pairwise F_ST = 0.004 and 0.002, respectively), and assignment tests were able to allocate 77% of the fish in these two historical groupings to the contemporary Okanogan River and Lake Wenatchee ESUs. A third historical genetic grouping was most closely aligned with contemporary sockeye salmon in Redfish Lake, Idaho, although the association was less robust (pairwise F_ST = 0.060). However, a fourth genetic grouping did not appear to be related to any contemporary sockeye salmon or kokanee population, assigned poorly to the O. nerka baseline, and had distinctive early return migration timing, suggesting that this group represents a historical ESU originating in headwater lakes in British Columbia that was probably extirpated sometime after 1924. The lack of a contemporary O. nerka population possessing the genetic legacy of this extinct ESU indicates that efforts to reestablish early‐migrating sockeye salmon to the headwater lakes region of the Columbia River will be difficult.     

Effects of eutrophication and temperature on Cyclotella rhomboideo‐elliptica Skuja,endemic diatom to China

An endemic diatom, Cyclotella rhomboideo‐elliptica Skuja, from the Yunnan Plateau, has been disappearing gradually from some lakes of the plateau. This study investigated the diatom's distribution in 30 lakes and documents long‐term population changes in the paleolimnological record of a deep lake, Lake Fuxian. Living cells of C. rhomboideo‐elliptica were found in five Yunnan Plateau lakes in 1957, but cells were restricted to Lake Fuxian in 2005. Its absolute abundance fluctuated from low to high to low. Our study suggests that nutrient concentrations correlate with C. rhomboideo‐elliptica's s abundance and survival. We infer that the disappearance of C. rhomboideo‐elliptica in some lakes may be due to increased nutrient concentrations and the species may be indicators of low nutrients. During the study, we also found that decreased in the diatoms average long axis length after the early 1990s. This morphological change was likely due to higher nutrient concentrations or to the increase in temperature, or a combination of the two.     

Lake‐specific variation in growth,migration timing and survival of juvenile sockeye salmon Oncorhynchus nerka: separating environmental from genetic influences

Time series on juvenile life‐history traits obtained from sockeye salmon Oncorhynchus nerka were analysed to assess lake‐specific environmental influences on juvenile migration timing, size and survival of fish from a common gene pool. Every year for the past two decades, O. nerka have been spawned at a hatchery facility, and the progeny released into two lakes that differ in average summer temperatures, limnological attributes and growth opportunities. Juveniles reared in the warmer, more productive Crosswind Lake were larger and heavier as smolts compared to those from the cooler, less productive Summit Lake and had higher in‐lake and subsequent marine survival. Crosswind Lake smolts migrated from the lake to sea slightly earlier in the season but the migration timing distributions overlapped considerably across years. Fry stocking density had a negative effect on smolt length for both lakes, and a negative effect on in‐lake survival in Summit Lake. Taken together, the results revealed a strong effect of lake‐rearing environment on the expression of life‐history variation in O. nerka. The stocking of these lakes each year with juveniles from a single mixed‐source population provided a large‐scale reverse common‐garden experiment, where the same gene pool was exposed to different environments, rather than the different gene pools in the same environment approach typical of evolutionary ecology studies. Other researchers are encouraged to seek and exploit similar serendipitous situations, which might allow environmental and genetic influences on ecologically important traits to be distinguished in natural or semi‐natural settings.     

Effects of river temperature and climate warming on stock‐specific survival of adult migrating Fraser River sockeye salmon (Oncorhynchus nerka)

Mean summer water temperatures in the Fraser River (British Columbia, Canada) have increased by ～1.5 °C since the 1950s. In recent years, record high river temperatures during spawning migrations of Fraser River sockeye salmon (Oncorhynchus nerka) have been associated with high mortality events, raising concerns about long‐term viability of the numerous natal stocks faced with climate warming. In this study, the effect of freshwater thermal experience on spawning migration survival was estimated by fitting capture–recapture models to telemetry data collected for 1474 adults (captured in either the ocean or river between 2002 and 2007) from four Fraser River sockeye salmon stock‐aggregates (Chilko, Quesnel, Stellako‐Late Stuart and Adams). Survival of Adams sockeye salmon was the most impacted by warm temperatures encountered in the lower river, followed by that of Stellako‐Late Stuart and Quesnel. In contrast, survival of Chilko fish was insensitive to the encountered river temperature. In all stocks, in‐river survival of ocean‐captured sockeye salmon was higher than that of river‐captured fish and, generally, the difference was more pronounced under warm temperatures. The survival–temperature relationships for ocean‐captured fish were used to predict historic (1961–1990) and future (2010–2099) survival under simulated lower river thermal experiences for the Quesnel, Stellako‐Late Stuart and Adams stocks. A decrease of 9–16% in survival of all these stocks was predicted by the end of the century if the Fraser River continues to warm as expected. However, the decrease in future survival of Adams sockeye salmon would occur only if fish continue to enter the river abnormally early, towards warmer periods of the summer, as they have done since 1995. The survival estimates and predictions presented here are likely optimistic and emphasize the need to consider stock‐specific responses to temperature and climate warming into fisheries management and conservation strategies.     

Thirty‐two single nucleotide polymorphism markers for high‐throughput genotyping of sockeye salmon

We characterize 32 single nucleotide polymorphism genotyping assays for resolving genotypic variation in sockeye salmon Oncorhynchus nerka in the Pacific Rim. These assays are based on the 5′‐nuclease reaction and thus facilitate high‐throughput genotyping with minimal optimization time. Minor allele frequency differences (Δq) among collections were between 4.7% and 97.9%, resulting in per locus F_ST estimates of 0.02–0.71 with an average of 0.22.     

Microbial eukaryote plankton communities of high‐mountain lakes from three continents exhibit strong biogeographic patterns

Microbial eukaryotes hold a key role in aquatic ecosystem functioning. Yet, their diversity in freshwater lakes, particularly in high‐mountain lakes, is relatively unknown compared with the marine environment. Low nutrient availability, low water temperature and high ultraviolet radiation make most high‐mountain lakes extremely challenging habitats for life and require specific molecular and physiological adaptations. We therefore expected that these ecosystems support a plankton diversity that differs notably from other freshwater lakes. In addition, we hypothesized that the communities under study exhibit geographic structuring. Our rationale was that geographic dispersal of small‐sized eukaryotes in high‐mountain lakes over continental distances seems difficult. We analysed hypervariable V4 fragments of the SSU rRNA gene to compare the genetic microbial eukaryote diversity in high‐mountain lakes located in the European Alps, the Chilean Altiplano and the Ethiopian Bale Mountains. Microbial eukaryotes were not globally distributed corroborating patterns found for bacteria, multicellular animals and plants. Instead, the plankton community composition emerged as a highly specific fingerprint of a geographic region even on higher taxonomic levels. The intraregional heterogeneity of the investigated lakes was mirrored in shifts in microbial eukaryote community structure, which, however, was much less pronounced compared with interregional beta‐diversity. Statistical analyses revealed that on a regional scale, environmental factors are strong predictors for plankton community structures in high‐mountain lakes. While on long‐distance scales (>10 000 km), isolation by distance is the most plausible scenario, on intermediate scales (up to 6000 km), both contemporary environmental factors and historical contingencies interact to shift plankton community structures.     

Tendencies of Density Dynamics in Reophilic and Lacustrine Sockeye Salmon Oncorhynchus nerkain the Basin of Azabach'e Lake

Temporal series of density in the spawners of two sockeye salmon populations from Azabach'e Lake (Kamchatka River basin) were analyzed using periodic functions. It has been found that the quality of describing the density dynamics for sockeye salmon by such models is very high (R ²= 0.943 and R ²= 0.905 for early and late populations, respectively). The density (for early sockeye salmon) and total number (for late sockeye salmon) distributions of the reproductive fraction of the populations have been developed and analyzed.     

Pacific Salmon,Nutrients, and the Dynamics of Freshwater and Riparian Ecosystems

Pacific salmon (Oncorhynchus spp.) accumulate substantial nutrients in their bodies as they grow to adulthood at sea. These nutrients are carried to predominantly oligotrophic lakes and streams, where they are released during and after spawning. Research over more than 3 decades has shown that the annual deposition of salmon-borne marine-derived nutrients (MD-nutrients) is important for the productivity of freshwater communities throughout the Pacific coastal region. However, the pathways and mechanisms for MD-nutrient transfer and accumulation in freshwater and riparian ecosystems remain virtually unexplored, consequently, there are many uncertainties in this area. This article addresses three related topics. First, we summarize recent advances in our understanding of the linkages among MD-nutrients, freshwater (including riparian) ecosystems, and community dynamics by addressing the importance of MD-nutrients to lakes and streams and by then reviewing large-scale and long-term processes in the atmosphere and ocean that govern variability in salmon populations. Second, we evaluate the validity of the discoveries and their implications for active ecosystem management, noting areas where extrapolation from these results still requires great caution. Finally, we outline five key research issues where additional discoveries could greatly augment our understanding of the processes shaping the structure and dynamics of salmon populations and the characteristics of their freshwater habitat and associated riparian zones. Collectively, the data suggest that the freshwater portion of the salmon production system is intimately linked to the ocean. Moreover, for the system to be sustainable, a holistic approach to management will be required. This holistic approach will need to treat climate cycles, salmon, riparian vegetation, predators, and MD-nutrient flowpaths and feedbacks as an integrated system. Received 3 July 2001; accepted 14 December 2001.     

Algal picoplankton production and contribution to food-webs in oligotrophic British Columbia lakes

The pelagic communities of two contrasting oligotrophic lakes in British Columbia were studied to determine why an interior, dimictic lake (Quesnel) supports a greater biomass of zooplankton and produces larger planktivorous sockeye salmon (Oncorhynchus nerka) than a coastal warm-monomictic lake (Sproat). The ultra-oligotrophic status and differing planktivore densities in Sproat Lake increased the relative importance of algal picoplankton, diminished the abundance of large zooplankton, and increased the significance of rotifers and other small-bodied zooplankton. These picoplankton based food webs result in longer, indirect and less efficient pathways of carbon flow from phytoplankton to fish. In contrast, Quesnel Lake is a more productive oligotrophic lake and its pelagic food webs are based more on nanoplankton and small microphytoplankton that support larger-bodied zooplankton (Daphnia, Diaptomus), and a more direct and efficient two-step transfer to fish. The greater variability of the annual recruitment of sockeye fry in interior lakes may keep zooplankton communities in a non-steady state, this in turn may perpetuate the occurrence of quadrennial cyclic dominance in adult salmon returning to these systems.     

THE INFLUENCE OF SUBMERGED MACROPHYTES ON SEDIMENTARY DIATOM ASSEMBLAGES1

Submerged macrophytes are a central component of lake ecosystems; however, little is known regarding their long‐term response to environmental change. We have examined the potential of diatoms as indicators of past macrophyte biomass. We first sampled periphyton to determine whether habitat was a predictor of diatom assemblage. We then sampled 41 lakes in Quebec, Canada, to evaluate whether whole‐lake submerged macrophyte biomass (BiomEpiV) influenced surface sediment diatom assemblages. A multivariate regression tree (MRT) was used to construct a semiquantitative model to reconstruct past macrophyte biomass. We determined that periphytic diatom assemblages on macrophytes were significantly different from those on wood and rocks (ANOSIM R = 0.63, P < 0.01). A redundancy analysis (RDA) of the 41‐lake data set identified BiomEpiV as a significant (P < 0.05) variable in structuring sedimentary diatom assemblages. The MRT analysis classified the lakes into three groups. These groups were (A) high‐macrophyte, nutrient‐limited lakes (BiomEpiV ≥525 μg · L^?1; total phosphorus [TP] <35 μg · L^?1; 23 lakes); (B) low‐macrophyte, nutrient‐limited lakes (BiomEpiV <525 μg · L^?1; TP <35 μg · L^?1; 12 lakes); and (C) eutrophic lakes (TP ≥35 μg · L^?1; six lakes). A semiquantitative model correctly predicted the MRT group of the lake 71% of the time (P < 0.001). These results suggest that submerged macrophytes have a significant influence on diatom community structure and that sedimentary diatom assemblages can be used to infer past macrophyte abundance.