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1) R.T. Paine's "Predation Begets Diversity?" Paradigm
Revisiting Paine's 1966 Sea Star Removal Experiment, the Most-Cited Empirical Article in The American Naturalist. Lafferty & Suchanek 2016
(see # 70 in Primary Literature list)
Abstract: “Food Web Complexity and Species Diversity” (Paine 1966) is the most-cited empirical article published in the American Naturalist. In short, Paine removed predatory sea stars (Pisaster ochraceus) from the rocky intertidal and watched the key prey species, mussels (Mytilus californianus), crowd out seven subordinate primary space-holding species. However, because these mussels are a foundational species, they provide three-dimensional habitat for over 300 associated species inhabiting the mussel beds; thus, removing sea stars significantly increases community-wide diversity. In any case, most ecologists cite Paine (1966) to support a statement that predators increase diversity by interfering with competition. Although detractors remained skeptical of top-down effects and keystone concepts, the paradigm that predation increases diversity spread. By 1991, “Food Web Complexity and Species Diversity” was considered a classic ecological paper, and after 50 years it continues to influence ecological theory and conservation biology.
2) Ocean Acidification - Mussel Shell Thinning
Historical Baselines and the Future of Shell Calcification for a Foundation Species in a Changing Ocean. Pfister et al. 2016
(see #69 in Primary Literature list)
Abstract: Seawater pH and the availability of carbonate ions are decreasing due to anthropogenic carbon dioxide emissions, posing challenges for calcifying
marine species. Marine mussels are of particular concern given their role as foundation species worldwide. Here, we document shell growth and
calcification patterns in
Mytilus californianus, the California mussel, over millennial and decadal scales. By comparing shell thickness across the largest modern shells, the largest mussels collected in the 1960s–1970s and shells from two Native American midden sites (1000–2420 years BP), we found that
modern shells are thinner overall, thinner per age category and thinner per unit length. Thus, the largest individuals of this species are calcifying less now than in the past. Comparisons of shell thickness in smaller individuals over the past 10–40 years, however, do not show significant shell thinning. Given our sampling strategy, these results are unlikely to simply reflect within-site variability or preservation effects. Review of environmental and biotic drivers known to affect shell calcification suggests declining ocean pH as a likely explanation for the observed shell thinning. Further future decreases in shell thickness could have significant negative impacts on M. californianus survival and, in turn, negatively impact the species-rich complex that occupies mussel beds.
3) The Mytilus californianus Mussel Bed Community
Extreme biodiversity in the marine environment: mussel
bed communities of Mytilus californianus. Suchanek 1992.
(see #28 in Primary Literature list)
Abstract: The exposed rocky intertidal component of Pacific Northwest shorelines is dominated by structurally complex beds of the interttidal mussel Mytilus californianus. These beds are componsed of (1) a physical matrix of interconnected living and dea mussel shells that may occur as a single layer or multiple layers (up to 5 or 6 mussel layers deep); (2) a layer of accumulated sediiments componsed of organic and shell debris; and (3) a diverse assemblage of plants and animals associated with the mussels which represents one of the most diverse temperate communities described to date - more than 300 taxa.
4) Mercury Cycling and Bioaccumulation
The Legacy of Mercury Cycling From Mining Sources in an Aquatic Ecosystem: From Ore To Organism. Suchanek et al. 2008 (see #51 in Primary Literature list)
Abstract. Clear Lake is the site of an abandoned mercury (Hg) mine (active intermittently from 1873 to 1957), now a U.S. Environmental Protection Agency Superfund Site. Mining activities, including bulldozing waste rock and tailings into the lake, resulted in 100 metric tons of Hg entering the lake’s ecosystem. This series of papers represents the culmination of 15 years of Hg related studies on this ecosystem, following Hg from the ore body to the highest trophic levels. A series of physical, chemical, biological, and limnological studies elucidate how ongoing Hg loading to the lake is influenced by acid mine drainage and how wind-driven currents and baroclinic circulation patterns redistribute Hg throughout the lake. Methylmercury (MeHg) production in this system is controlled by both sulfate-reducing bacteria as well as newly identified iron-reducing bacteria. Sediment cores (dated with dichlorodiphenyldichlorethane [DDD], 210-Pb, and 14-C) to 250 cm depth (representing up to 3000 years before present) elucidate a record of Total Hg (TotHg) loading to the lake from natural sources and mining and demonstrate how methyl mercury (MeHg) remains stable at depth within the sediment column for decades to millenia. Core data also identify other stresses that have influenced the Clear Lake Basin especially over the past 150 years. Although Clear Lake is one of the most Hg-contaminated lakes in the world, biota do not exhibit MeHg concentrations as high as would be predicted based on the gross level of Hg loading. We compare Clear Lake’s TotHg and MeHg concentrations with other sites worldwide and suggest several hypotheses to explain why this discrepancy exists. Based on our data, together with state and federal water and sediment quality criteria, we predict potential resulting environmental and human health effects and provide data that can assist remediation efforts.
5) Mass Balance Mercury Budget for Clear Lake
A Mass Balance Mercury Budget for a Mine- Dominated Lake: Clear Lake, California. Suchanek et al., 2009
(see #64 in Primary Literature list)
Abstract: The Sulphur Bank Mercury Mine (SBMM), active intermittently from 1873–1957 and now a USEPA Superfund site, was previously estimated to have contributed at least 100 metric tons (105 kg) of mercury (Hg) into the Clear Lake aquatic ecosystem. We have confirmed this minimum estimate. To better quantify the contribution of the mine in relation to other sources of Hg loading into Clear Lake and provide data that might help reduce that loading, we analyzed Inputs and Outputs of Hg to Clear Lake and Storage of Hg in lakebed sediments using a mass balance approach. We evaluated Inputs from (1) wet and dry atmospheric deposition from both global/regional and local sources, (2) watershed tributaries, (3) groundwater inflows, (4) lakebed springs and (5) the mine. Outputs were quantified from (1) efflux (volatilization) of Hg from the lake surface to the atmosphere, (2) municipal and agricultural water diversions, (3) losses from out-flowing drainage of Cache Creek that feeds into the California Central Valley and (4) biotic Hg removal by humans and wildlife. Storage estimates include (1) sediment burial from historic and prehistoric periods (over the past 150–3,000 years) from sediment cores to ca. 2.5m depth dated using dichloro diphenyl dichloroethane (DDD), 210Pb and 14C and (2) recent Hg deposition in surficial sediments. Surficial sediments collected in October 2003 (11 years after mine site remediation) indicate no reduction (but a possible increase) in sediment Hg concentrations over that time and suggest that remediation has not significantly reduced overall Hg loading to the lake. Currently, the mine is believed to contribute ca. 322–331 kg of Hg annually to Clear Lake, which represents ca. 86–99% of the total Hg loading to the lake. We estimate that natural sedimentation would cover the existing contaminated sediments within ca. 150–300 years.
6) Impacts of the Exxon Valdez Oil Spill
Shoreline impacts in the Gulf of Alaska region following the Exxon Valdez oil spill. Gilfillan et al. 1995
(see #32 in Primary Literature list)

Abstract: Forty-eight sites in the Gulf of Alaska region (GOA-Kodiak Island, Kenai Peninsula, and Alaska Peninsula) were sampled in July/August 1989 to assess the impact of the March 24, 1989 Exxon Valdez Oil Spill (EVOS) on shoreline chemistry and biological communities hundreds of miles from the spill origin. In a 1990 companion study, 5 of the Kenai sites and 13 of the Kodiak and Alaska Peninsula sites were sampled 16 months after the spill. Oiling levels at each site were estimated visually and/or quantified by chemical analysis. The chemical analyses were performed on sediment an/or rock wipe samples collected with the biological samples. Additional sediment samples were collected for laboratory amphipod toxicity tests.  Mussels were also collected and analyzed for hydrocarbon content to assess hydrocarbon bioavailability.  Biological investigations at these GOA sites focused on intertidal infauna, epifauna, and macroalgae by means of a variety of common ecological techniques. For rocky sites the percentage of hard substratum covered y biota was quantified. At each site, up to 5 biological samples (scrapes of rock surfaces or sediment cores) were collected intertidally along each of 3 transects, spanning tide levels from the high intertidal to mean-lowest-low-water (zero tidal datum). Organisms (down to 1.0mm in size) from these samples were sorted and identified. Community parameters including organisms abundance, species richness, and Shannon diversity were calculated for each sample.

7) Farallon Islands Nuclear Waste Dump Site
Radionuclides in Fishes and Mussels from the Farallon Islands Nuclear Waste Cump Site, California. Suchanek et al. 1996
(see #34 in Primary Literature list)

Abstract: The Farallon Islands Nuclear Waste Dump Site (FINWDS), approximately 30 miles west of San Francisco, California, received at least 500 TBq encapsulated in more than 47,500 containers from approximately 1945 to 1970. During several seasons in 1986/87 deep-sea bottom feeding fishes (Dover sole = Microstomus pacificus; sablefish = Anoplopoma fimbria; thornyheads = Sebastolobus spp.) and intertidal mussels (Mytilus californianus) were collected from the vicinity of the FINWDS and from comparable depths at a reference site near Point Arena, CA.  Tissues were analyzed for several radionuclides (137-Cs, 238-Pu, 239+240-Pu and 241-Am). Radionuclide concentrations for fish and mussel tissue ranged from non-detectable to 4,340 mBq kg-1 wet weight, with the following means for Farallon fishes: 137-Cs = 1,110 mBq kg-1; 238-Pu = 390 mBq kg-1; 239+240-Pu = 130 mBq kg-1; and 241-Am = 1,350 mBq-1. There were no statistically significant differences in the radionuclide concentrations observed in samples from the Farallon Islands compared to reference samples from Point Arena, CA. Concentrations of both 238Pu and 241Am in fish tissues (from both sites) were notably higher than those reported in literature from any other sites worldwide, including potentially contaminated sites. Concentrations of 239+240-Pu from both sites were typical of low values found at some contaminated sites worldwide. These results show ~10 times higher concentrations of 239+240-Pu and ~40-50 times higher concentrations of 238-Pu than those values reported for identical fish species from 1977 collections at the FINWDS. Radionuclide concentrations were converted to a hypothetical per capita annual radionuclide intake for adults, yielding the following values of annual Committed Effective Dose Equivalent (CEDE) from ionizing radiation emitted from these radionuclides: 0.000 mSv y-1 for 137-Cs, 0.009 mSv y-1 for 238-Pu, and 0.003 mSv y-1 for 239+240-Pu. For 241-Am, projected CEDE for Dover sole, sablefish, and thornyheads were higher, averaging 0.03 mSv y-1. The observed isotopic ratio of 238-Pu/239+240-Pu was about 4 (which is two orders of magnitude higher than the ratio of 0.03 associated with fallout from weapons tests and accidental releases in the north temperate zone of the earth), indicating a considerably higher environmental mobilization for 238-Pu compared to 239+240-Pu. Likewise, the observed ratio of 241-Am/239+240-Pu of about 30 was nearly two orders of magnitude higher than the fallout ratio of 0.43 in the north temperate zone of the earth. The projected ionizing radiation CEDE to people from the ingestion of fish with fallout radionuclides was three times higher for 241Am than from the plutonium isotopes.

8) Bioturbation in tropical lagoons
Control of seagrass communities and sediment distribution by Callianassa (Crustacea, Thalassinidea) bioturbation.
Suchanek 1983
(see #11 in Primary Literature list)
Abstract: Shallow tropical lagoons at St. Croix, U.S. Virgin Islands were found to have high densities of the ghost shrimp Callianassa spp. The ecology of four species of Callianassa is discussed: C. acanthochirus, C. longiventris, C. rathbunae and C. quadracuta. The first two species capture and store in their burrows drifting detritus of seagrass and algae. The latter two species build volcano-shaped mounds of ejected sediment during feeding and burrowing. Massive quantities of sediment (up to 2.59 kg/mo/day) are funneled into subsurface galleries, gleaned for organic material and sorted. Fine grains « 1.4 mm diam.) are then pumped back up to the surface forming mounds. Coarse-grained material (~ 1.4 mm) such as shell debris and coral fragments are not pumped back to the surface, but are stored in many deep chambers which extend> 1.5 m below the sediment surface. In cross-section, cores from high Callianassa mound density regions show distinct alternating coarse and fine layers. This sedimentological evidence could be used as an indicator of Callianassa activity when interpreting the geological record from ancient tropical lagoonal environments. Maximum seagrass productivity and percent cover are negatively correlated (significant to p < .01) with Callianassa mound density. Experimental and control transplants of the turtle grass Thalassia testudinum into regions of high (16/m2) and low (11m') Callianassa mound density produced a dramatic deterioration of Thalassia within 2-4 months in high density Callianassa areas. Ejected sediment either reduces available light for photosynthesis or physically smothers Thalassia, thereby eliminating it from regions of abundant Callianassa. Because seagrass communities have such intimate energetic ties to other nearby shallow-water and deep-sea communities, the negative influence of Callianassa on seagrass beds is suspected to have second and third order effects on other tropical communities as well.
Response of primary space occupiers and associated community species richness to sea star removal at Tatoosh Island, WA.
Shell thickness of mussels from the Olympic Peninsula, WA, showing declines from indian midden shells (1,000-2,000 yrs ago), versus archived shells (1970s-1990s) versus modern shells (2000s), likely due to ocean acidification. 
Diagram representing the diverse community of  over 300 species of organisms associated with the mussel
bed matrix of Mytilus californianus.
Movement of total mercury and methylmercury in the physical and biological components of the Clear Lake aquatic ecosystem.
Mercury inputs, outputs and storage within the Clear Lake aquatic ecosystem.
Time lapse spread of oil from the grounding of the the Exxon Valdez oil tanker in Prince William Sound in 1989.
A simplified food web asssociated with bottom feeding fishes (Dover sole, sablefish, thornyheads) exposed to the radionuclides Cesium-137, Plutonium -238, Plutonium- 239+240, and Americium-241 at the Farallon Islands Nuclear Waste Dump Site.
Diagram of callianassid mounds and sub-sediment burrow complex reconstructed from resin casts .