The yellow perch (Perca flavescens) fishery of the Les Cheneaux Islands region of Lake Huron experienced an unprecedented collapse in 2000. Immediately prior to the collapse was the proliferation of double-crested cormorants (Phalacrocorax auritus) in the area. Subsequent investigations established that double-crested cormorant predation was chief among the forces shaping the local yellow perch population and contributing to the collapse of the fishery. A double-crested cormorant control program was implemented in 2004 with the objective of benefiting the yellow perch population and fishery. This study used creel survey and gillnet fish community assessment data to evaluate the response of the yellow perch population and fishery. In all, seven key yellow perch metrics were analyzed using regression analysis with double-crested cormorant abundance as the independent variable. As double-crested cormorant abundance declined, yellow perch abundance increased, total mortality rate decreased, the angler catch rate and harvest in the recreational fishery improved, yellow perch growth rate declined and mean age increased. Increased yellow perch recruitment was documented since 2003 but it was the longevity of these year classes, (improved survival) as much or more than their magnitude of the year class, that allowed for the progress towards recovery. Questions facing managers are the sustainable level of double-crested cormorants in the region and the long term prognosis for the yellow perch fishery to fully recover to pre—double—crested cormorant levels.

Diverse management techniques have been used to mitigate conflicts between humans and double-crested cormorants (Phalacrocorax auritus) including harassment methods supplemented by lethal take. In this study we evaluated impacts of programs to harass spring migrating cormorants on the walleye (Sander vitreus) fishery in Brevoort Lake and the yellow perch (Perca flavescens) and walleye fisheries at Drummond Island. Cormorant foraging declined significantly (p<0.05) at both locations subsequent to initiation of harassment programs. Overall harassment deterred 90% of cormorant foraging attempts while taking less than 6% lethally on average at each site. Yellow perch were a predominate prey item in number and biomass at both locations. Walleye made up a small proportion of the diet at both locations. However, both walleye and yellow perch abundance increased significantly (p<0.05) at Drummond Island. Walleye abundance at age 3 increased to record levels in 2008 following 3 years of cormorant management at Brevoort Lake. The estimated cormorant consumption of age-1 walleye in the absence of management at Brevoort Lake during 2005 would account for 55% of the record 2006 age-1 walleye population. These results support the hypothesis that cormorant predation on spawning aggregations of sportfish was a significant mortality factor and cormorant management reduced sportfish mortality and increased abundance at both locations. Continuation of harassment programs and fishery assessments will determine whether improvement of targeted sport fisheries through control of spring migrating cormorants is sustainable.

The yellow perch fishery of the Les Cheneaux Islands (LCI) region of Lake Huron, MI suffered a collapse in 2000, attributed in part to the increase of double-crested cormorants (Phalacrocorax auritus) in the region. A management program involving egg-oiling and lethal culling was initiated in 2004 to reduce cormorant foraging on yellow perch in the LCI. Counts of cormorant nests, nests oiled, cormorants culled, and aerial counts and telemetry surveys were used to evaluate management. Management contributed to a 74% reduction of cormorants on breeding colonies from 2004 to 2007. Cormorants used the LCI area significantly more (P<0.05) than surrounding areas. Aerial counts of foraging cormorants declined significantly (P<0.05) over the entire survey area but not within the LCI proper. However, aerial counts of cormorants in the LCI were five-fold less than cormorant counts in the same area in 1995. Reduced cormorant numbers were attributed in part to the elimination of cormorant nesting on a large colony due to the introduction of raccoons. Although the numbers of cormorants using the LCI did not decline, flocks were significantly smaller and more dispersed after management began. The reduced number of cormorants from 1995 levels and more dispersed foraging likely reduced predation on fish stocks including yellow perch in the LCI. Our findings indicate that the relationship between reduction in cormorant breeding numbers and reduced cormorant foraging in a given area is complex and may be influenced by density dependent factors such as intraspecific competition and quality of the forage base.

The Great Lakes form the largest freshwater island system in the world and provide breeding habitat for a large proportion of the continental population of double-crested cormorants (Phalacrocorax auritus). Here, cormorants have a high profile due to conflicts with humans; by 2007, most active (64%) breeding sites in U.S. waters were managed. This study used data from the U.S. Great Lakes Colonial Waterbird Database and The Nature Conservancy's Great Lakes Island GIS database to identify important features of breeding sites in the U.S. Great Lakes and broaden understanding of cormorant presence at the island-landscape scale. Islands 0.5–10 ha were used more frequently than expected, and most sites had remoteness values of ≤3km. Colony size was positively correlated with years occupied and large colonies (>1000 pairs) developed primarily (95%) on island sites >1.0 ha. Sites supporting large colonies were more remote than those supporting smaller colonies. Presence of other colonial waterbird species, especially Herring Gulls (Larus argentatus), also characterized cormorant sites. Islands used by cormorants comprised a small proportion (n = 90, 3%) of the U.S. Great Lakes island resource, and <1% of the total island area. Certain characteristics of breeding sites (e.g., small islands, proximity to mainland) may increase negative attitudes about cormorants. To understand cormorant impacts to island resources (e.g., vegetation; other colonial waterbird species), we suggest cormorant presence in the Great Lakes be considered in the broader context of island science, conservation and known threats, and at a landscape scale.

The proliferation of the invasive round goby (Apollonia melanostoma) in the Great Lakes has caused shifts in the trophic ecology in some areas. We examined the diet of double-crested cormorants (Phalacrocorax auritas) prior to, and immediately after, round goby population expansion at two colonies, Pigeon and Snake Islands, in eastern Lake Ontario from 1999 to 2007. Cormorant diet was determined from the examination of 10,167 pellets collected over the nine-year period. By the second year round gobies were found in the diet (2002 at Snake Island and 2003 at Pigeon Island) they were the main species consumed by cormorants at each colony. The dominance of round goby in cormorant diets had a significant effect on both daily fish consumption and seasonal trends in fish consumption compared to the pre-goby years. Seasonal differences that were observed during the pre-goby years were lost once gobies became the main diet component of cormorants. The rapid switch to a benthic prey such as round goby, from a largely limnetic fish diet demonstrates the adaptive foraging ability of cormorants. Round goby may act as a buffer for yellow perch and smallmouth bass, two sport fish impacted by cormorant predation in eastern Lake Ontario.

Nuisance growth of the attached, green alga Cladophora was considered to have been abated by phosphorus management programs mandated under the Great Lakes Water Quality Agreement. The apparent resurgence of nuisance growth in Lakes Erie, Michigan and Ontario has been linked conceptually to ecosystem alterations engineered by invasive dreissenid mussels (Dreissena polymorpha and Dreissena bugensis). Here, we apply contemporary modeling tools and historical water quality data sets in quantifying the impact of long-term changes in phosphorus loading and dreissenid-mediated changes in water clarity on the distribution and production of Cladophora. It is concluded that reductions in phosphorus loading in the predreissenid period achieved the desired effect, as model simulations were consistent with the biomass declines reported from the early 1970s to the early 1980s. These declines were, however, largely offset by dreissenid-driven changes in water clarity that extended the depth of colonization by Cladophora, increasing total production. We were not able to isolate and quantify the significance of dreissenid mediation of phosphorus cycling using the historical database. Phosphorus management remains the appropriate mechanism for reducing nuisance levels of Cladophora growth. The development of action plans will require an improved understanding of nearshore phosphorus dynamics such as might be obtained through regular monitoring of soluble reactive phosphorus levels, internal phosphorus content and Cladophora biomass in impacted nearshore regions of the Great Lakes.

The impacts of large-scale, episodic sediment resuspension on the cycling of polychlorinated biphenyl congeners (PCBs) were examined using a spatially coordinated air and water sampling strategy conducted in southern Lake Michigan in the late winters of 1998, 1999, and 2000. We found no significant temporal changes in gas phase, dissolved phase, or suspended sediment PCB concentrations despite large-scale seasonal storms occurring before and after sampling campaigns. Only gas phase and suspended sediment PCBs varied spatially. Higher total suspended material (TSM) concentrations and fraction organic carbon (f_oc) were measured at sampling stations located in the near-shore region of southern Lake Michigan than at open-water sampling stations. Gas phase concentrations (ΣPCB_g) were higher in the west (0.436 ± 0.200 ng/m³, n = 11) and south (0.408±0.286 ng/m³, n = 5) than the east (0.214±0.082 ng/m³, n = 10) and central (0.253 ± 0.145 ng/m³, n = 8) regions of southern Lake Michigan. Dissolved phase concentrations (ΣPCB_d) averaged 0.18±0.024 ng/L (n = 52); suspended sediment concentrations (ΣPCB_s) accounted for between 4% and 72% (23 ± 4%, n = 52) of the total ΣPCB concentrations (ΣPCB_T = ΣPCB_d ΣPCB_s). Despite no consistent temporal variations in both dissolved phase or suspended sediment ΣPCB concentrations, there were temporal and spatial variations in the distribution shift between phases that can be linked to sediment resuspension, not a state of equilibrium. Specifically, our analysis suggests sediment resuspension results in preferential sorption of heavier, more chlorinated PCB congeners.

Concentrations of polychlorinated biphenyls (PCBs) were measured in composited samples of walleyes Sander vitreus and their prey during 2005–2007 from Saginaw Bay, Lake Huron. There was a linear relationship between fish length and PCB concentrations in walleyes between 356 and 608 mm, but fish 680 mm had lesser concentrations than 608-mm fish. When fish 222–550 mm from 1990 were compared with those from 2007, there was a decrease of 1315 ng PCBs/g wet wt (ww). Concentrations of PCBs in gizzard shad Dorosoma cepedianum (190 ng PCBs/g ww) were three-fold less than fish collected in 1990 (516 ng PCBs/g ww). Round gobies Neogobius melanostomus collected from the Saginaw River had the greatest concentrations of PCBs (range: 200–350 ng PCBs/g ww) compared with other prey fishes (45–190 ng PCBs/g ww). Concentrations of PCBs in Saginaw River round gobies were three-fold greater than those from Saginaw Bay. Zooplankton from 1990 and 2008 contained 8.0 and 32 ng PCBs/g ww, respectively, while zebra mussels Dreissena polymorpha from 2008 contained 351 ng PCBs/g ww. Principal components analysis showed that PCB congeners differed between the largest walleyes and other fish. There are several possible explanations for lesser concentrations of PCBs observed in 2007. These include effects of dredging, changes in the food web related to round gobies, loss of alewife Alosa pseudoharengus, which was a major walleye prey item in 1990, and replacement by yellow perch Perca flavescens, or decreases in release of PCBs from sediments due to weathering, burial, or diffusion.

Perfluoroalkyl acids (PFAs) are a family of highly persistent compounds which are present in the environment as a result of degradation of polyfluorinated precursors, from use as processing aids for production of fluoropolymers, and use in fire fighting foams. The purpose of this study was to investigate prevailing concentrations and possible sources of PFAs in Lake Superior, as well as in Siskiwit Lake on Isle Royale. Between 2001 and 2005, replicate water samples were taken from lake surface waters, and from depth profiles, as well as from major tributaries including municipal waste water treatment plants (WWTPs) at three major population centers. Perfluorooctanoate (PFOA) was the predominant PFA in Lake Superior, with concentrations ranging from 0.07 to 1.2 ng/L in surface waters. PFOA concentrations were generally 1.5 to 2-fold greater than perfluorooctanesulfonate (PFOS) levels. WWTPs were found to contribute up to 20 fold higher concentrations of PFOA (22 ng/L) relative to the intake water from Lake Superior, while most tributaries contained lower concentrations of perfluorocarboxylates (PFCA) and perfluoroalkylsulfonates (PFSs) (<0.1 ng/L). Overall tributaries and precipitation were estimated to be the major sources of PFCAs and PFSs to Lake Superior. Tributaries were estimated to be the largest source contributing 59% of PFOA and 57% of PFOS inputs to the lake. Profiles conducted over the deepest points in the lake showed that PFAs were found throughout the water column, however, there was no distinctive trend with depth.

A recent review of the Great Lakes Water Quality Agreement has concluded that while controls on phosphorus inputs to Lake Michigan achieved the desired effect in offshore waters, the nearshore region continues to suffer from elevated phosphorus levels. Failure to achieve trophic state goals in the nearshore is manifested in nuisance growth of Cladophora and attendant impacts on property owners, utilities, and the public health and welfare. This study focuses on a site in Lake Michigan near Milwaukee, Wisconsin, where nuisance growth of Cladophora and associated beach fouling occur regularly. A mechanistic model simulating Cladophora growth, suitable for guiding nutrient management in the Great Lakes nearshore, is presented. The model represents an update of the Canale and Auer framework, reflecting current understandings of Cladophora ecology and offering a user-friendly interface making the software more widely available to decision makers. This Great Lakes Cladophora Model (GLCM) is first validated for the Auer/Canale data set collected in 1979 at a site on Lake Huron and then for a data set developed in 2006 for a site on Lake Michigan. Model performance under the strikingly different forcing conditions (depth, light, phosphorus levels) characteristic of these two sites affirms the widespread applicability of the tool. The GLCM is then extended to examine the impacts of ecosystem perturbation (dreissenid colonization) on Cladophora growth and to future approaches to monitoring and management.

Algal carotenoids (n:16) and chlorophylls (n:7) were determined in phytoplankton (n:60), filamentous algae (n:14) and sediments (n:44), collected from two nearshore sites in eastern Lake Erie (Van Buren Point (VBP), 6.5 m; Point Gratiot (PG), 17 m), during summer and fall of 2003, 2004 and 2005. The most prominent biomarkers for diatoms (fucoxanthin), cryptophytes (alloxanthin), chlorophytes (chlorophyll-b) and cyanobacteria (zeaxanthin) revealed temporal variations in phytoplankton community composition, which were correlated to water temperatures: i) seasonal succession, from diatoms with some cryptophytes in June (cool), to an increased percentage of chlorophytes and cyanobacteria in August and September (warm); ii) differences between 2004 (cool; cryptophytes more abundant) and 2005 (warm; chlorophytes more abundant). Filamentous algae (chlorophytes, epiphytic diatoms; some cyanobacteria) varied in condition, according to levels of chl-a, pheopigments, and class biomarkers: high, at VBP (growing; decaying; bont/E suspect); low, at PG (mostly dead). Relative to phytoplankton, sediments were depleted in several biomarkers (chl-a; diadino-, neo- and violaxanthin) but enriched with others, particularly at PG (pheopigments; diatoxanthin; canthaxanthin, echinenone; alloxanthin). Sediment composition was characterized by strong differences between sites (chl-a, chl-b and fucoxanthin nearly 10-fold greater at VBP than PG) and increasing accumulation of biomarkers from year-to-year. A linear log-log function, relating total carotenoids to total chlorophylls (intercept -0.516, slope 1.054, r² 0.96), implied increased biodegradation among specimen types: levels of pigments (pmol/g ww) decreased three orders of magnitude, from phytoplankton, through filamentous algae, to sediments. Deviation from a 1:1 relationship indicated 1.7-fold depletion of carotenoids relative to chlorophylls at mid-range.

We used analyses of burbot (Lota lota) and lake trout (Salvelinus namaycush) diets taken during spring gillnet surveys in northern Lake Michigan in 2006–2008 to investigate the potential for competition and predator-prey interactions between these two species. We also compared our results to historical data from 1932. During 2006–2008, lake trout diet consisted mainly of alewives (Alosa pseudoharengus) and rainbow smelt (Osmerus mordax), whereas burbot utilized a much wider prey base including round goby (Neogobius melanostomus), rainbow smelt, alewives, and sculpins. Using the Schoener's diet overlap index, we found a higher potential for interspecific competition in 1932 than in 2006–2008, though diet overlap was not significant in either time period. No evidence of cannibalism by lake trout or lake trout predation on burbot was found in either time period. In 2006–2008, however, lake trout composed 5.4% (by weight) of burbot diet. To determine whether this predation could be having an impact on lake trout rehabilitation efforts in northern Lake Michigan, we developed a bioenergetic-based consumption estimate for burbot on Boulder Reef (a representative reef within the Northern Refuge) and found that burbot alone can consume a considerable proportion of the yearling lake trout stocked annually, depending on burbot density. Overall, we conclude that predation, rather than competition, is the more important ecological interaction between burbot and lake trout, and burbot predation may be contributing to the failed lake trout rehabilitation efforts in Lake Michigan.

Sediment cores from Lake Qarun provide a record of mid-late Holocene climatic changes in Northern and Eastern Africa as well as environmental changes due to the activities of ancient Egyptians. We used sedimentological, mineralogical, and geochemical analyses of the cores to investigate long-term variations in lake level due to changing hydrologic inputs. An age model based on three paired 14C and paleomagnetic measurements suggests that the base of the sediment cores is as old as ∼5000 B.C.E. Geochemical analyses indicated that lake sediments were derived from Nile floods with an admixture of Saharan sand. Laminated endogenic carbonate-rich clayey silt lithofacies with benthic diatoms are indicative of relatively low lake levels, saline waters and dry conditions; massive lithofacies with planktonic diatom species are indicative of relatively high lake levels, fresh waters and humid conditions. Faintly laminated clayey silt lithofacies suggest intermediate conditions. Variations in lithology as well as diatom composition suggest that the lake level has varied from relatively high levels in its early history to lower levels in later years although there have been numerous cycles in water level over the past 7000 years. A combination of climate changes in the source area of the Nile River as a result of monsoon dynamics; climatic changes in the setting area of the Lake Qarun; and human activities through the dynasties in Egypt produced these variations in lake level.

Walleye (Sander vitreus) is an important sport fish in the Great Lakes that is experiencing low reproductive success after severe population declines starting in the late 1940s. In the Muskegon River, Michigan, natural reproduction of walleyes remains low and is largely supplemented by stocking. To determine factors influencing walleye reproductive success in the Muskegon River, we estimated walleye egg survival using in situ egg incubators covered with nitex screening (2003–2004) and estimated density and survival of fertilized eggs caught on furnace filter traps across different substrate types (2005–2006). We compared physical habitat suitability for walleye eggs under high and low flow scenarios. Density of walleye eggs was highest in regions of gravel/cobble substrates. Egg survival was higher in egg incubators (24–49.5%) than on furnace filter traps (2.0%), suggesting predation is an important source of walleye egg mortality in the Muskegon River. Cold water temperatures that extended developmental stage durations may also be an important source of egg mortality. The dynamic habitat suitability model predicted low suitability for eggs due to poor temperature and velocity conditions. Despite low egg survival rates, 40 million to 1 billion eggs were estimated to hatch. The low natural reproduction of walleyes in the Muskegon River is likely due to a combination of low walleye egg survival and failure of walleye larvae to reach their nursery grounds in Muskegon Lake.

This 12-year study of Hexagenia male imagos documents the recovery of two species of burrowing mayflies, Hexagenia limbata and Hexagenia rigida in western Lake Erie after a 30-year absence due to hypoxia, resulting from cultural eutrophication. Annual adult mayfly collections were made at night during the peak emergence period at four sites along the north shore of the western basin of Lake Erie, 1997 to 2008. H. rigida, the dominant species in upstream riverine waterbodies, was the early colonizer, representing about 90% of all male imagos sampled in 1997. In 2000, when the two species were co-dominant, both inland aerial dispersal (5.5 km) and lakeward (0.25 to 4 km) oviposition patterns confirmed species co-existence. Twice weekly collections throughout the extended emergence period at one site confirmed that H. rigida was the dominant species in 1997, H. limbata and H. rigida were co-dominant in 2000, and H. limbata was dominant in 2002. Once H. limbata became the dominant species (>90%) in 2000 to 2002 (depending on the site), it remained so. Both species followed a similar inland dispersal pattern, decreasing in density with increasing distance from shore; most mayflies were present within 1 km from shore. There was no significant difference in mean egg density of the two species among the sites extending lakeward in 2000 when the two species were equally abundant. The transition from the dominance of H. rigida to H. limbata may have resulted from several factors, including differential competition and growth between species or predation effects.

zooplankton production plays a critical role in the Great Lakes ecosystem, and vertical migration, which is exhibited by many zooplankton species, could affect production. We examined the effects of water temperature and food resource gradients on the growth rate of zooplankton undergoing vertical migration in Lake Michigan. In three laboratory experiments, juvenile Daphnia mendotae, native herbivorous cladocerans, were incubated for 5 days at water temperatures associated with the epilimnion and deep chlorophyll maxima (DCM) of Lake Michigan and were fed food resources collected directly from these regions. Growth rate strongly depended on water temperature, as Daphnia incubated at the epilimnetic temperature (21 °C) grew 42% faster than those at the DCM temperature (8 °C). Growth rate of Daphnia that alternated between the two temperatures every 12 h (0.108 day^-1) was similar to the arithmetic average growth rate of the two water temperature treatment extremes (0.110 day^-1), suggesting fluctuating temperatures alone do not substantially influence Daphnia growth. In contrast, food resources derived from different depths did not affect growth rate, nor was there a significant interaction between food resource origin and water temperature effects. Our results indicate that vertical migration will reduce growth rate, and hence zooplankton production, through reduced temperature, not from changes in resources. Consideration of the effects of vertical migration, especially given the known variability in this behavior, may substantially improve zooplankton production estimates in the Great Lakes.

The benthic amphipod Diporeia represents a crucial trophic link that conveys vital nutrients and energy to predators at higher trophic levels. The current decline of Diporeia populations, mostly in the North American Great Lakes, may, in part, be related to concurrent declines in food quantity and/or quality. We hypothesized that somatic growth and survival of Diporeia would be positively related to dietary supply and subsequent retention of polyunsaturated fatty acids (PUFA); a class of chemicals known to affect diet quality. We examined how different algal PUFA concentrations in; a) Ankistrodesmus falcatus (Chlorophyta), b) a naturally occurring diatom assemblage from Lake Ontario, c) a non-toxic strain of Microcystis aeruginosa (Cyanophyta), and, d) fasting for 30 d, affected PUFA concentrations, somatic growth, and survival of Diporeia. Total PUFA concentrations were significantly higher in A. falcatus than in diatoms and Microcystis, but only diatoms contained considerable amounts of eicosapentaenoic (EPA) and docosahexaenoic acid (DHA). EPA, DHA, and arachidonic acid (ARA) were highly retained in Diporeia even in the absence of dietary supply with ARA being the most efficiently bioaccumulated PUFA. Survivorship of Diporeia ranged from 60% (diatom-fed), 68% (A. falcatus-fed), to 70% (fasting treatment), but was 0% in the M. aeruginosa diet treatment. Nucleic acid ratios (RNA:DNA), commonly used as proxies for somatic growth potential, were highest in Diporeia feeding on diatoms and lowest in fasting animals. We conclude that overall condition of Diporeia improved with dietary access to EPA and DHA, but survival was not related to this food quantity and/or quality.

Human-induced degradation of coastal wetlands often leads to altered trophic dynamics and species assemblages. Here we use data from 77 coastal marshes in three Laurentian Great Lakes collected between 2001 and 2007 to examine the relationship between human disturbance (road density and wetland quality) and characteristics of aquatic turtle assemblages, including species richness and abundances. Painted turtles (Chrysemys picta) were encountered disproportionately in degraded wetlands and the probability of occurrence decreased with improved site quality. Abundance of painted turtles peaked, however, at intermediate road density in surrounding 1- and 2-km buffers. Across all sites, species richness was highest and common snapping turtles (Chelydra serpentina) were most abundant in wetlands with intermediate water quality. The common musk turtle (Sternotherus odoratus) was absent from degraded wetlands in the lower lakes (Erie and Ontario) that fell within their historical range, but reached high abundances in marshes of Georgian Bay and the North Channel, a region with relatively low human disturbance. Analysis of sex ratios in painted turtles revealed a significant male bias in an area with high road density, while the sex ratio did not differ significantly from 1:1 in a less developed region, consistent with reports of high female mortality in urban areas.

Middle Island sinkhole (23 m depth) is an underwater karst feature in Lake Huron (MI, USA) inundated with hypoxic, high-conductivity groundwater. Here, microbial mats composed of purple-pigmented filamentous cyanobacteria cover carbon-rich sediments. To study the species diversity of Archaea and Eukarya in this habitat, we constructed clone libraries and sequenced the small subunit ribosomal RNA genes from sediment cores sectioned into five visually distinct layers: the surface cyanobacterial mat (0–0.2 cm), an underlying white crystalline layer (0.2–0.5 cm), and three sub-sections of black organic-rich sediment chosen from distinct layers in the cores (0.5–2.0 cm, 7.5–9.5 cm, and 24.5–28.5 cm). Clone libraries from the cyanobacterial mat were dominated by eukaryal 18S rRNA gene sequences such as nematodes (Tobrilus gracilis), ciliates (Frontonia vernalis), and tardigrades (Isohypsibius granulifer). Shallow organic-rich sediments shared clones with the overlying mat but also included seed shrimp (Cyprididae sp.) and copepods (Leptodiaptomus spp.). Clone libraries from the deepest sediments were dominated by archaeal sequences similar to known methanogens (Methanosphaerula and Methanosaeta) and uncultivated Archaea, including non-thermophilic Crenarchaeota. Phylogenetic trees revealed representation in diverse eukaryotic and archaeal lineages. By chronicling the species composition of freshwater sinkholes, this study expands our knowledge of microbial communities in habitats influenced by hypoxic, sulfur-rich groundwater.

Diporeia hoyi and Mysis relicta are the most important prey items of slimy sculpins (Cottus cognatus) in the Great Lakes. Slimy sculpins were collected from dreissenid-infested bottoms off seven Lake Michigan ports at depths of 27–73 m in fall 2003 to study their lake-wide diets. Relatively large dreissenid biomass occurred at depths of 37- and 46-m. Quagga mussels (Dreissena bugnesis) composed at least 50% of dreissenid biomass at Manistique, Saugatuck, and Sturgeon Bay. Mysis accounted for 82% of the sculpin diet by dry weight at eastern Lake Michigan while Diporeia composed 54–69% of the diet at western Lake Michigan and dominated the diets of slimy sculpins at all sites deeper than 46 m. In northern Lake Michigan, this diet study in new sites showed that slimy sculpin consumed more prey with low energy contents, especially chironomids, than Mysis and Diporeia in shallow sites (depth <55 m). We recommend diet studies on sedentary benthic fishes to be conducted along perimeters of the Great Lakes to observe changes in their diets that may be impacted by changing benthic macroinvertebrate communities.

Lake trout Salvelinus namaycush fry treated with heated water to create thermal marks in their otoliths were stocked at Sve's Reef in Minnesota waters of Lake Superior in 1994, 1995, and 1996. These fish began to reach maturity in 2000, and were vulnerable to annual assessment gill nets set at several locations along the Minnesota shoreline. Captured fish also included fin-clipped lake trout stocked as yearlings, and naturally reproduced (wild) lake trout. Otoliths from 3106 undipped lake trout were aged and examined for thermal marks from 2000 to 2007, of which 1152 were from the target year classes (1994–1996). Thermal marks were found in otoliths from 64 fish, or 5.6% of those in the target year classes, demonstrating that stocked fry contributed to the adult lake trout population in Minnesota waters. Although numbers of recaptured fish were too low to demonstrate statistically significant differences, higher recapture rates of marked fish at Sve's Reef in fall and spawning assessments suggest that these fish may have imprinted at the stocking location and homed back to this area to spawn. Wild lake trout populations in Lake Superior may be approaching fully rehabilitated levels, but recovery in the lower Great Lakes has progressed more slowly, and evidence of success with fry stocking could benefit those populations.

Non-native migratory salmonids ascend tributaries to spawn in all the Great Lakes. In Lake Ontario, these species include Chinook salmon (Oncorhynchus tshawytscha), coho salmon (O. kisutch), steelhead (O. mykiss), and brown trout (Salmo trutta). Although successful natural reproduction has been documented for many of these species, little research has been conducted on their spawning habitat. We examined the spawning habitat of these four species in the Salmon River, New York. Differences in fish size among the species were significantly correlated with spawning site selection. In the Salmon River, the larger species spawned in deeper areas with larger size substrate and made the largest redds. Discriminant function analysis correctly classified redds by species 64–100% of the time. The size of substrate materials below Lighthouse Hill Dam is within the preferred ranges for spawning for these four species indicating that river armoring has not negatively impacted salmonid production. Intra-specific and inter-specific competition for spawning sites may influence redd site selection for smaller salmonids and could be an impediment for Atlantic salmon (S. salar) restoration.

Long-term systematic storage of environmental specimens has become an important component of formal environmental monitoring programs in many countries. In 1977, the Contaminants Surveillance Program (CSP) began in the Great Lakes Basin. In support of the CSP, Fisheries and Oceans Canada began archiving fish tissue samples and created the Great Lakes Fisheries Specimen Bank (GLFSB). In 2006, responsibility for the GLFSB was transferred to Environment Canada and it was renamed the National Aquatic Biological Specimen Bank (NABSB). The new name better reflects the current contents and purpose of the specimen bank which now supports Canada's Chemicals Management Plan (CMP). The NABSB employs standardized banking protocols, computerized sample tracking, maintenance of all data and metadata associated with each specimen, and modern storage equipment situated in a dedicated facility at the Canada Centre for Inland Waters in Burlington, Ontario. Since 1977, specimens from the NABSB have contributed to more than 60 scientific publications, reports, and/or book chapters on the status, trends, and bioaccumulation of metals and various organic contaminants such as PCBs, dioxins, furans, and aromatic hydrocarbons, in aquatic ecosystems. Collection and archiving of specimens in the NABSB continues such that the specimen bank currently holds more than 52,000 samples from 18,749 specimens of top predator fish, forage fish, plankton, and other invertebrates collected over 32 years of environmental monitoring in the Canadian waters of the Great Lakes and beyond.