Monitoring microbes in the Great Lakes.

Great Lakes environmental agencies want to build the capacity to understand microbe threats and develop responses and mitigation plans in advance of crises such as large fish kills. We developed a collaborative plan for monitoring microbes across the Great Lakes of North America to meet practical needs with the latest science and testing technology. The goal was to build understanding of harmful microbes and be rapid, relevant, and robust in addressing threats. The program was oriented for adaptability to changing threats and will target areas of human activity, especially shipping ports and invasion hotspots. Sampling will be aimed at fish and water with application of molecular testing procedures that will allow rapid, efficient, and very sensitive detection of microbes. Compared to other programs with similar aims, our agenda is broader in scope, focuses on building knowledge, uses a representative sampling design, and will provide findings for proactive management and response planning. The reliance on molecular testing procedures, sample archiving, and rapid and broadly distributed results distinguishes our approach from the other similar programs. Fitting microbe monitoring into the Great Lakes environmental management agenda is expected to add an important new dimension to ecosystem monitoring and yield new knowledge of importance for management.

A water quality model for regional stream assessment and conservation strategy development.

Non-point-source (NPS) pollution remains the primary source of stream impairment in the United States. Many problems such as eutrophication, sedimentation, and hypoxia are linked with NPS pollution which reduces the water quality for aquatic and terrestrial organisms. Increasingly, NPS pollution models have been used for landscape-scale pollution assessment and conservation strategy development. Our modeling approach functions at a scale between simple landscape-level assessments and complex, data-intensive modeling by providing a rapid, landscape-scale geographic information system (GIS) model with minimal data requirements and widespread applicability. Our model relies on curve numbers, literature-derived pollution concentrations, and land status to evaluate total phosphorus (TP), total nitrogen (TN), and suspended solids (SS) at the reach scale. Model testing in the Chesapeake Bay watershed indicated that predicted distributions of water quality classes were realistic at the reach scale, but precise estimates of pollution concentrations at the local scale can have errors. Application of our model in the tributary watersheds along Lake Ontario suggested that it is useful to managers in watershed planning by rapidly providing important information about NPS pollution conditions in areas where large data gaps exist, comparisons among stream reaches across numerous watersheds are required, or regional assessments are sought.

Fish communities in coastal freshwater ecosystems: the role of the physical and chemical setting.

BACKGROUND: We explored how embayment watershed inputs, morphometry, and hydrology influence fish community structure among eight embayments located along the southeastern shoreline of Lake Ontario, New York, USA. Embayments differed in surface area and depth, varied in their connections to Lake Ontario and their watersheds, and drained watersheds representing a gradient of agricultural to forested land use. RESULTS: We related various physicochemical factors, including total phosphorus load, embayment area, and submerged vegetation, to differences in fish species diversity and community relative abundance, biomass, and size structure both among and within embayments. Yellow perch (Perca flavescens) and centrarchids numerically dominated most embayment fish communities. Biomass was dominated by piscivorous fishes including brown bullhead (Ameiurus nebulosus), bowfin (Amia calva), and northern pike (Esox lucius). Phosphorus loading influenced relative biomass, but not species diversity or relative abundance. Fish relative abundance differed among embayments; within embayments, fish abundance at individual sampling stations increased significantly with submerged vegetative cover. Relative biomass differed among embayments and was positively related to total phophorus loading and embayment area. Fish community size structure, based on size spectra analysis, differed among embayments, with the frequency of smaller-bodied fishes positively related to percent vegetation. CONCLUSION: The importance of total phosphorus loading and vegetation in structuring fish communities has implications for anthropogenic impacts to embayment fish communities through activities such as farming and residential development, reduction of cultural eutrophication, and shoreline development and maintenance.

Abundance exchange models of fish assemblages along the Hudson River Estuary Gradient, New York.

The spatially explicit abundance exchange model (AEM) was built for four fish species: winter flounder (Pseudopleuronectes americanus), Atlantic silverside (Menidia menidia), eastern silvery minnow (Hybognathus regius), and striped bass (Morone saxatilis) along the Hudson River estuary gradient, New York. The fish and habitat data during 1974-1997 were used to develop and calibrate the AEM; and the fish data during 1998-2001 was used to validate the model. Preference indexes of fish species for dissolved oxygen, salinity, water temperature, and bottom substrates along the gradient were estimated; and these were used to compute habitat preference (HP) of the associated fish species. The species HP was a key variable in the AEM to quantify abundance and distribution patterns of the associated species along the gradient. The AEM could efficiently predict abundance and distribution patterns of all modeled species except striped bass. The model ability for predicting a local distribution range of a fish species with broad tolerance on changing environment like striped bass should be improved.

Fish Assemblage Recovery Along a Riverine Disturbance Gradient.

Artificial fluctuations in streamflow have been documented to alter the composition and structure of stream communities. This study tests the hypothesis that a spatial recovery gradient in fish assemblage structure exists downstream of a hydroelectric dam, and that recovery can be identified by the presence and abundance of species largely restricted to flowing-water habitats (fluvial specialists). A longitudinal gradient of change in a shoreline fish assemblage was quantified in a 66-km reach of a mid-sized, species-rich river (Tallapoosa River, Alabama) with daily flow fluctuations from hydropower generation. The shoreline fish assemblage in a nearby and similar river (Cahaba River, Alabama) was quantified as a regional reference for the occurrence of fish assemblage gradients. Fish were collected with prepositioned area electrofishers in 240 randomly located sampling sites, and physical habitat was quantified. Using distributional and habitat use information, fish species were categorized as fluvial specialists or macrohabitat generalists (species that occur in a wide variety of aquatic systems). Sampled habitats were similar between rivers and along each study reach. The longitudinal pattern of species occurrence and fish abundance was consistent in the free-flowing river. A longitudinal gradient of increasing abundance and richness of only fluvial specialist species existed downstream of the hydroelectric dam. No similar spatial gradient existed for macrohabitat generalists in either river. Although a fish community recovery gradient was identified, a recovery endpoint was not evident because assemblage change was gradual and possibly incomplete. The preservation and management of riverine fish faunas will partly depend on incorporating spatial recovery into decisions about permitting and siting of anthropogenic changes like hydroelectric dams.

Low prevalence of Cyprinid Herpesvirus 3 Found in common carp (Cyprinus carpio carpio) collected from nine locations in the Great Lakes.

Cyprinid herpesvirus 3 (CyHV3) is a viral disease of fish first detected in the United States in 1998. Since that time, mortality events in common carp (Cyprinus carpio carpio) have occurred in several locations within the Great Lakes basin, but not within the Great Lakes themselves. We sampled 675 carp from 20 sites across the Great Lakes and Lake St. Clair, Michigan, USA, between 19 July and 26 September 2010. We tested the gill and a pooled internal organ sample from each fish for CyHV3 with the use of a quantitative polymerase chain reaction (qPCR) assay. Virus was detected in 18 fish from nine sites in four lakes (Lakes Michigan, Huron, St. Clair, and Ontario). Tissues from these 18 fish were also tested for CyHV3 with the use of the PCR assay recommended by the World Organization for Animal Health; amplification was achieved from two fish and confirmation by sequencing of CyHV3 from one fish collected in Lake St. Clair. The results of this study suggest that CyHV3 is present in the Great Lakes.

Detection of viral hemorrhagic septicemia virus by quantitative reverse transcription polymerase chain reaction from two fish species at two sites in Lake Superior.

Viral hemorrhagic septicemia virus (VHSV) was first detected in the Laurentian Great Lakes in 2005 during a mortality event in the Bay of Quinte, Lake Ontario. Subsequent analysis of archived samples determined that the first known isolation of VHSV in the Laurentian Great Lakes was from a muskellunge Esox masquinongy collected in Lake St. Clair in 2003. By the end of 2008, mortality events and viral isolations had occurred in all of the Laurentian Great Lakes except Lake Superior. In 2009, a focused disease surveillance program was designed to determine whether VHSV was also present in Lake Superior. In this survey, 874 fish from 7 sites along the U.S. shoreline of Lake Superior were collected during June 2009. Collections were focused on nearshore species known to be susceptible to VHSV. All fish were dissected individually by using aseptic techniques and were tested for the presence of VHSV genetic material by use of a quantitative reverse transcription (qRT) polymerase chain reaction (PCR) targeting the viral nucleoprotein gene. Seventeen fish from two host species at two different sites tested positive at low levels for VHSV. All attempts to isolate virus in cell culture were unsuccessful. However, the presence of viral RNA was confirmed independently in five fish by using a nested PCR that targeted the glycoprotein (G) gene. Partial G gene sequences obtained from three fish were identical to the corresponding sequence from the original 2003 VHSV isolate (MI03) from muskellunge. These detections represent the earliest evidence for the presence of VHSV in Lake Superior and illustrate the utility of the highly sensitive qRT-PCR assay for disease surveillance in aquatic animals.

Distribution of an invasive aquatic pathogen (viral hemorrhagic septicemia virus) in the Great Lakes and its relationship to shipping.

Viral hemorrhagic septicemia virus (VHSV) is a rhabdovirus found in fish from oceans of the northern hemisphere and freshwaters of Europe. It has caused extensive losses of cultured and wild fish and has become established in the North American Great Lakes. Large die-offs of wild fish in the Great Lakes due to VHSV have alarmed the public and provoked government attention on the introduction and spread of aquatic animal pathogens in freshwaters. We investigated the relations between VHSV dispersion and shipping and boating activity in the Great Lakes by sampling fish and water at sites that were commercial shipping harbors, recreational boating centers, and open shorelines. Fish and water samples were individually analyzed for VHSV using quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and cell culture assays. Of 1,221 fish of 17 species, 55 were VHSV positive with highly varied qRT-PCR titers (1 to 5,950,000 N gene copies). The detections of VHSV in fish and water samples were closely associated and the virus was detected in 21 of 30 sites sampled. The occurrence of VHSV was not related to type of site or shipping related invasion hotspots. Our results indicate that VHSV is widely dispersed in the Great Lakes and is both an enzootic and epizootic pathogen. We demonstrate that pathogen distribution information could be developed quickly and is clearly needed for aquatic ecosystem conservation, management of affected populations, and informed regulation of the worldwide trade of aquatic organisms.

Integrated ecosystem assessment: Lake Ontario water management.

BACKGROUND: Ecosystem management requires organizing, synthesizing, and projecting information at a large scale while simultaneously addressing public interests, dynamic ecological properties, and a continuum of physicochemical conditions. We compared the impacts of seven water level management plans for Lake Ontario on a set of environmental attributes of public relevance. METHODOLOGY AND FINDINGS: Our assessment method was developed with a set of established impact assessment tools (checklists, classifications, matrices, simulations, representative taxa, and performance relations) and the concept of archetypal geomorphic shoreline classes. We considered each environmental attribute and shoreline class in its typical and essential form and predicted how water level change would interact with defining properties. The analysis indicated that about half the shoreline of Lake Ontario is potentially sensitive to water level change with a small portion being highly sensitive. The current water management plan may be best for maintaining the environmental resources. In contrast, a natural water regime plan designed for greatest environmental benefits most often had adverse impacts, impacted most shoreline classes, and the largest portion of the lake coast. Plans that balanced multiple objectives and avoided hydrologic extremes were found to be similar relative to the environment, low on adverse impacts, and had many minor impacts across many shoreline classes. SIGNIFICANCE: The Lake Ontario ecosystem assessment provided information that can inform decisions about water management and the environment. No approach and set of methods will perfectly and unarguably accomplish integrated ecosystem assessment. For managing water levels in Lake Ontario, we found that there are no uniformly good and bad options for environmental conservation. The scientific challenge was selecting a set of tools and practices to present broad, relevant, unbiased, and accessible information to guide decision-making on a set of management options.

Recovery of a US endangered fish.

BACKGROUND: More fish have been afforded US Endangered Species Act protection than any other vertebrate taxonomic group, and none has been designated as recovered. Shortnose sturgeon (Acipenser brevirostrum) occupy large rivers and estuaries along the Atlantic coast of North America, and the species has been protected by the US Endangered Species Act since its enactment. METHODOLOGY/PRINCIPAL FINDINGS: Data on the shortnose sturgeon in the Hudson River (New York to Albany, NY, USA) were obtained from a 1970s population study, a population and fish distribution study we conducted in the late 1990s, and a fish monitoring program during the 1980s and 1990s. Population estimates indicate a late 1990s abundance of about 60,000 fish, dominated by adults. The Hudson River population has increased by more than 400% since the 1970s, appears healthy, and has attributes typical for a long-lived species. Our population estimates exceed the government and scientific population recovery criteria by more than 500%, we found a positive trend in population abundance, and key habitats have remained intact despite heavy human river use. CONCLUSIONS/SIGNIFICANCE: Scientists and legislators have called for changes in the US Endangered Species Act, the Act is being debated in the US Congress, and the Act has been characterized as failing to recover species. Recovery of the Hudson River population of shortnose sturgeon suggests the combination of species and habitat protection with patience can yield successful species recovery, even near one of the world's largest human population centers.