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Assessing macroinvertebrate biodiversity in freshwater ecosystems: Advances and challenges in dna-based approaches

Assessing the biodiversity of macroinvertebrate fauna in freshwater ecosystems is an essential component of both basic ecological inquiry and applied ecological assessments. Aspects of taxonomic diversity and composition in freshwater communities are widely used to quantify water quality and measure the efficacy of remediation and restoration efforts. The accuracy and precision of biodiversity assessments based on standard morphological identifications are often limited by taxonomic resolution and sample size. Morphologically based identifications are laborious and costly, significantly constraining the sample sizes that can be processed. We suggest that the development of an assay platform based on DNA signatures will increase the precision and ease of quantifying biodiversity in freshwater ecosystems. Advances in this area will be particularly relevant for benthic and planktonic invertebrates, which are often monitored by regulatory agencies. Adopting a genetic assessment platform will alleviate some of the current limitations to biodiversity assessment strategies. We discuss the benefits and challenges associated with DNA-based assessments and the methods that are currently available. As recent advances in microarray and next-generation sequencing technologies will facilitate a transition to DNA-based assessment approaches, future research efforts should focus on methods for data collection, assay platform development, establishing linkages between DNA signatures and well-resolved taxonomies, and bioinformatics. ?? 2010 by The University of Chicago Press.

The Quarterly Review of Biology

A model for evaluation of sediment exposure and burial for freshwater mussels from heavy particle sedimentation

Freshwater mussels (Bivalvia: Unionida) are an ecologically important faunal group. Excessive sediments, both in suspended and deposited formats, are believed to have negative effects on survival of freshwater mussels. However, there is a lack of quantitative tools for assessing the impact of abrupt and excessive sedimentation on freshwater mussel habitats. This gap in knowledge poses challenges for construction planning that necessitates evaluating sedimentation effects on mussels. In this paper, we present a simple Lagrangian particle tracking (LPT) model designed to investigate the downstream distances from the sediment release point where mussels may face risks of sediment exposure and burial during episodic sedimentation events. We validated the model in predicting the deposition of sands ranging from 125 to 625 μ m "> 625μm in diameter within an open channel. Subsequently, we applied the LPT model to a representative stretch of mussel habitats in the lower Osage River, Missouri, USA. Implementing the LPT model using computational fluid dynamics analysis of river hydrodynamics, we investigated the downstream distances impacted by a hypothetical sedimentation event. The results indicate that the mussels within tens and hundreds of meters may be at risk of burial under low and high flow conditions, respectively. Mussels within hundreds and potentially thousands of meters may be at risks of sediment exposure under low and high flow conditions, respectively. The impacted distance is highly dependent on the sediment diameters and flow conditions. These results contribute valuable insights into the potential impacts of sedimentation on freshwater mussel habitats, aiding in informed decision-making for construction projects near these critical aquatic ecosystems.

Ecological Modelling

Biogeography of freshwater mussels (Bivalvia: Unionida) in Texas and implications on conservation biology

Aim Biogeography seeks to identify and explain the spatial distributions of species and has become an important tool used by conservationists to protect and manage aquatic organisms. Texas, located in the southwestern United States, is home to 52 species of freshwater mussels, 9 of which are endemic to Texas and 7 that are endemic to Texas and neighboring states or countries. There have been two major attempts to classify this fauna into biogeographical provinces; however, both efforts relied on limited distribution information and outdated taxonomy. To address both issues, we set out to delineate biogeographic provinces for freshwater mussels in Texas by using a comprehensive distributional dataset of >28,000 records and molecular information. Location Southwestern United States. Methods We compiled community and molecular data for 48 of the 52 freshwater mussel species that occur in Texas. We performed algorithmic hierarchal cluster analysis (HCA) and nonmetric multidimensional scaling (NMDS) based on Euclidean distance to identify biogeographic groupings. We conducted a similar analysis using molecular sequence data for our target species. Results Based on the results from community and molecular data, we identified seven biogeographic provinces for freshwater mussels in Texas: Great Plains, Mississippi Embayment, Sabine-Neches, Trinity-San Jacinto, Central Texas, Rio Grande and Coastal. However, the Coastal and Great Plains provinces were not included in our analysis and were recognized based on previous work. Main conclusions Our approach integrating community and molecular datasets provides a comprehensive assessment of the biogeography of freshwater mussels in Texas, which serves as a model for future biogeographic studies. Our findings also shed light on the ecological, evolutionary and geologic processes shaping freshwater mussel communities in Texas, which is important for the conservation of remaining biodiversity in the state.

Texas

Water budget for the Nueces Estuary, Texas, May-October 1998

The Texas Water Development Board (TWDB), Texas Parks and Wildlife Department (TPWD), and Texas Natural Resource Conservation Commission (TNRCC) are charged by the Texas Legislature with determining freshwater inflows required to maintain the ecological health of streams, bays, and estuaries in Texas. To determine required inflows, the three agencies collect data and conduct studies on the needs for freshwater inflows to Texas estuaries. The U.S. Geological Survey (USGS), in cooperation with the TWDB, conducted a study in the Nueces estuary (fig. 1) during May–October 1998 to provide water-budget data for calibration of a TWDB model that will be used to estimate the effects of different freshwater inflow volumes on circulation and salinity in the estuary. The water budget (inflows and outflows) for the Nueces estuary was estimated by using (1) data collected during this study, (2) data collected at two upstream streamflow-gaging stations previous to this study, and (3) evaporation and return-flow data obtained from other agencies. This fact sheet describes the data-collection methods and the results of the water-budget estimates for the Nueces estuary.

Texas

Computed discharges at five sites in lower Laguna Madre near Port Isabel, Texas, June 1997

The Texas Water Development Board (TWDB), Texas Parks and Wildlife Department (TPWD), and Texas Natural Resource Conservation Commission (TNRCC) are charged by the Texas Legislature with determining freshwater inflows required to maintain the ecological health of streams, bays, and estuaries in Texas. To determine required inflows, the three agencies collect data and conduct studies on the needs for freshwater inflows to estuaries. The TWDB uses estuarine hydrodynamic and conservativetransport computer models to predict the effects of altering freshwater inflows on estuarine circulation and salinity. To calibrate these models, a variety of water-quality and discharge data are needed.

Texas

Future water-supply scenarios, Cape May County, New Jersey, 2003-2050

Stewards of the water supply in New Jersey are interested in developing a plan to supply potable and non-potable water to residents and businesses of Cape May County until at least 2050. The ideal plan would meet projected demands and minimize adverse effects on currently used sources of potable, non-potable, and ecological water supplies. This report documents past and projected potable, non-potable, and ecological water-supply demands. Past and ongoing adverse effects to production and domestic wells caused by withdrawals include saltwater intrusion and water-level declines in the freshwater aquifers. Adverse effects on the ecological water supplies caused by groundwater withdrawals include premature drying of seasonal wetlands, delayed recovery of water levels in the water-table aquifer, and reduced streamflow. To predict the effects of future actions on the water supplies, three baseline and six future scenarios were created and simulated. Baseline Scenarios 1, 2, and 3 represent withdrawals using existing wells projected until 2050. Baseline Scenario 1 represents average 1998-2003 withdrawals, and Scenario 2 represents New Jersey Department of Environmental Protection (NJDEP) full allocation withdrawals. These withdrawals do not meet projected future water demands. Baseline Scenario 3 represents the estimated full build-out water demands. Results of simulations of the three baseline scenarios indicate that saltwater would intrude into the Cohansey aquifer as much as 7,100 feet (ft) to adversely affect production wells used by Lower Township and the Wildwoods, as well as some other near-shore domestic wells; water-level altitudes in the Atlantic City 800-foot sand would decline to -156 ft; base flow in streams would be depleted by 0 to 26 percent; and water levels in the water-table aquifer would decline as much as 0.7ft. [Specific water-level altitudes, land-surface altitudes, and present sea level when used in this report are referenced to the North American Vertical Datum of 1988 (NAVD 88).] Future scenarios 4 to 9 represent withdrawals and the effects on the water supply while using estimated full build-out water demands. In most townships, existing wells would be used for withdrawals in the simulation. However, in Lower and Middle Townships, the Wildwoods, and the Cape Mays, withdrawals from some wells would be terminated, reduced, or increased. Depending on the scenario, proposed production wells would be installed in locations far from the saltwater fronts, in deep freshwater aquifers, in deeper saltwater aquifers, or proposed injection wells would be installed to inject reused water to create a freshwater barrier to saltwater intrusion. Simulations indicate that future Scenarios 4 to 9 would reduce many of the adverse effects of Scenarios 1, 2, and 3. No future scenario will minimize all adverse impacts. In Scenario 4, Lower Township would drill two production wells in the Cohansey aquifer farther from the Delaware shoreline than existing wells and reduce withdrawals from wells near the shoreline. Wildwood Water Utility (WWU) would reduce withdrawals from existing wells in the Cohansey aquifer and increase withdrawals from wells in the Rio Grande water-bearing zone. Results of the simulation indicate that saltwater intrusion and ecological-water supply problems would be reduced but not as much as in Scenarios 5, 7, 8, and 9. In Scenario 5, the Wildwoods and Lower Township each would install a desalination plant and drill two wells to withdraw saltwater from the Atlantic City 800-foot sand. Saltwater intrusion problems would be reduced to the greatest extent with this scenario. Ecological water supplies remain constant or decline from 2003 baseline values. Water-level altitudes would decline to -193 ft in the Atlantic City 800-foot sand, the deepest potentiometric level for all scenarios. In Scenario 6, Lower Township would build a tertiary treatment system and drill three wells open to the Cohanse

New Jersey

Serrasalmidae — Piranhas and Pacus

The family Serrasalmidae is a morphologically and ecologically diverse group of South American freshwater fishes consisting of 16 genera and about 91 valid species. This chapter is a summary of the current state of knowledge on serrasalmid taxonomy, species richness, and ecology, and provides an identification key to the genera and references to relevant literature for species-level identifications. Included is information on native and non-native populations.

Book chapter

Development and assessment of fluorescent-dyed, preserved invasive grass carp (Ctenopharyngodon idella) eggs as surrogates for live eggs in transport and dispersal control experiments

Invasive species such as grass carp ( Ctenopharyngodon idella ) pose substantial ecological threats to North American freshwater ecosystems. Understanding their early life stage behavior is critical for management efforts. From spawning to hatching, invasive carp eggs must remain suspended in the water column while drifting downstream for the best chance of survival. This highly vulnerable life stage is a potential target for population control to reduce recruitment. However, studying egg transport and potential dispersal control techniques is challenging, because the availability of live eggs and time period for experimentation are extremely limited. Additionally, accurately replicating the physical characteristics and transport mechanisms of fish eggs using surrogates in laboratory and field studies is not trivial. This study presents a novel method to create fluorescein-dyed, preserved grass carp eggs as surrogates for live eggs in transport and dispersal control experiments. This technique enables year-round studies of grass carp egg transport, offering managers a reliable tool for developing and testing dispersal control and passive sampling methods for invasive carp eggs. In this study, we rehydrate and dye preserved grass carp eggs in varying concentrations of aqueous fluorescein for a range of rehydration times, evaluate dye retention and egg visibility under ultraviolet light (UV-A), and measure diameters and settling velocities for comparison with live eggs. Eggs rehydrated in 0.100 g per liter fluorescein for 30 min maintain adequate brightness for up to 40 min in mixed conditions and exhibit mean settling velocities and densities similar to live eggs, making them ideal for laboratory experiments using quantitative imaging techniques.

River Research and Applications

Relaxed selection causes microevolution of seawater osmoregulation and gene expression in landlocked Alewives

Ecological transitions from marine to freshwater environments have been important in the creation of diversity among fishes. Evolutionary changes associated with these transitions likely involve modifications of osmoregulatory function. In particular, relaxed selection on hypo-osmoregulation should strongly affect animals that transition into novel freshwater environments. We used populations of the Alewife ( Alosa pseudoharengus ) to study evolutionary shifts in hypo-osmoregulatory capacity and ion regulation associated with freshwater transitions. Alewives are ancestrally anadromous, but multiple populations in Connecticut have been independently restricted to freshwater lakes; these landlocked populations complete their entire life cycle in freshwater. Juvenile landlocked and anadromous Alewives were exposed to three salinities (1, 20 and 30 ppt) in small enclosures within the lake. We detected strong differentiation between life history forms: landlocked Alewives exhibited reduced seawater tolerance and hypo-osmoregulatory performance compared to anadromous Alewives. Furthermore, gill Na + /K + -ATPase activity and transcription of genes for seawater osmoregulation (NKCC—Na + /K + /2Cl − cotransporter and CFTR—cystic fibrosis transmembrane conductance regulator) exhibited reduced responsiveness to seawater challenge. Our study demonstrates that adaptations of marine-derived species to completely freshwater life cycles involve partial loss of seawater osmoregulatory performance mediated through changes to ion regulation in the gill.

Connecticut

Migrating ducks and submersed aquatic vegetation respond positively after invasive common carp (Cyprinus carpio) exclusion from a freshwater coastal marsh

Invasive carp can negatively affect waterbirds through habitat degradation, including removal of submersed aquatic vegetation (SAV). At a freshwater coastal marsh of great ecological and cultural significance, we excluded invasive common carp ( Cyprinus carpio ) with the goal of restoring the marsh to historical conditions to support fall-migrating waterfowl. We used a multi-pronged approach to assess the response of ducks and SAV to carp exclusion by leveraging historical duck and SAV surveys and collecting new data for six years post-exclusion on density and distribution of ducks within the marsh, SAV response, and refueling performance (as indexed by plasma-lipid metabolites) by two species of diving ducks. We found that fall-migrating duck numbers and total SAV extent rebounded to historical levels (1970s). There was a 339% increase in diving duck density and a nearly 400% increase in dabbling duck density between the pre- (i.e., 2000s) and post-exclusion periods. Diving ducks were more likely to be observed associated with SAV within the marsh, whereas dabbling ducks responded to emergent vegetation extent and water levels. Refueling performance was stable post-exclusion, despite increased numbers of ducks using the marsh, indicating that marsh habitat quality was sufficient. Some aspects of the marsh recovery remain in question, including possible shifts in SAV community composition. Overall, the carp exclusion has successfully improved the quality of habitat for migrating ducks.

Manitoba

Modeling water quality in the Anthropocene: Directions for the next-generation aquatic ecosystem models

“Everything changes and nothing stands still” (Heraclitus). Here we review three major improvements to freshwater aquatic ecosystem models — and ecological models in general — as water quality scenario analysis tools towards a sustainable future. To tackle the rapid and deeply connected dynamics characteristic of the Anthropocene, we argue for the inclusion of eco-evolutionary, novel ecosystem and social-ecological dynamics. These dynamics arise from adaptive responses in organisms and ecosystems to global environmental change and act at different integration levels and different time scales. We provide reasons and means to incorporate each improvement into aquatic ecosystem models. Throughout this study we refer to Lake Victoria as a microcosm of the evolving novel social-ecological systems of the Anthropocene. The Lake Victoria case clearly shows how interlinked eco-evolutionary, novel ecosystem and social-ecological dynamics are, and demonstrates the need for transdisciplinary research approaches towards global sustainability.

Current Opinion in Environmental Sustainability

Integrative phylogenetic, phylogeographic and morphological characterisation of the Unio crassus species complex reveals cryptic diversity with important conservation implications

The global decline of freshwater mussels and their crucial ecological services highlight the need to understand their phylogeny, phylogeography and patterns of genetic diversity to guide conservation efforts. Such knowledge is urgently needed for Unio crassus , a highly imperilled species originally widespread throughout Europe and southwest Asia. Recent studies have resurrected several species from synonymy based on mitochondrial data, revealing U. crassus to be a complex of cryptic species. To address long-standing taxonomic uncertainties hindering effective conservation, we integrate morphometric, phylogenetic, and phylogeographic analyses to examine species diversity within the U. crassus complex across its entire range. Phylogenetic analyses were performed using cytochrome c oxidase subunit I (815 specimens from 182 populations) and, for selected specimens, whole mitogenome sequences and Anchored Hybrid Enrichment (AHE) data on ∼600 nuclear loci. Mito-nuclear discordance was detected, consistent with mitochondrial DNA gene flow between some species during the Pliocene and Pleistocene. Fossil-calibrated phylogenies based on AHE data support a Mediterranean origin for the U. crassus complex in the Early Miocene. The results of our integrative approach support 12 species in the group: the previously recognised Unio bruguierianus , Unio carneus, Unio crassus , Unio damascensis , Unio ionicus , Unio sesirmensis , and Unio tumidiformis , and the reinstatement of five nominal taxa: Unio desectus stat. rev. , Unio gontierii stat. rev. , Unio mardinensis stat. rev. , Unio nanus stat. rev. , and Unio vicarius stat. rev. Morphometric analyses of shell contours reveal important morphospace overlaps among these species, highlighting cryptic, but geographically structured, diversity. The distribution, taxonomy, phylogeography, and conservation of each species are succinctly described.

Molecular Phylogenetics and Evolution

Diatoms in estuaries and tidal marshes

Diatoms from estuarine and marsh sediments can be used to evaluate a number of geological processes. Information on salinity, elevation, and substrate derived from modern assemblages have been used to determine local and regional Holocene sea level history, identify seismic and tsunami events, and aid in the recognition of regional variations in precipitation. In order to apply diatoms to these questions, it is necessary to have a detailed knowledge of the ecology of marine, brackish, and freshwater taxa, as well as an understanding of the taphonomic processes that determine the final diatom assemblage. The potential for studies of pre-Holocene estuarine depositional systems is largely limited by the availability of study sites.

The Paleontological Society Papers

Spatial dependence of reduced sulfur in Everglades dissolved organic matter controlled by sulfate enrichment

Sulfate inputs to the Florida Everglades stimulate sulfidic conditions in freshwater wetland sediments that affect ecological and biogeochemical processes. An unexplored implication of sulfate enrichment is alteration of the content and speciation of sulfur in dissolved organic matter (DOM), which influences the reactivity of DOM with trace metals. Here, we describe the vertical and lateral spatial dependence of sulfur chemistry in the hydrophobic organic acid fraction of DOM from unimpacted and sulfate-impacted Everglades wetlands using X-ray absorption spectroscopy and ultrahigh-resolution mass spectrometry. Spatial variation in DOM sulfur content and speciation reflects the degree of sulfate enrichment and resulting sulfide concentrations in sediment pore waters. Sulfur is incorporated into DOM predominantly as highly reduced species in sulfidic pore waters. Sulfur-enriched DOM in sediment pore waters exchanges with overlying surface waters and the sulfur likely undergoes oxidative transformations in the water column. Across all wetland sites and depths, the total sulfur content of DOM correlated with the relative abundance of highly reduced sulfur functionality. The results identify sulfate input as a primary determinant on DOM sulfur chemistry to be considered in the context of wetland restoration and sulfur and trace metal cycling.

Florida

Spatiotemporal associations of reservoir nutrient characteristics and the invasive, harmful alga Prymnesium parvum in West Texas

Golden alga ( Prymnesium parvum ) is a harmful alga that has caused ecological and economic harm in freshwater and marine systems worldwide. In inland systems of North America, toxic blooms have nearly eliminated fish populations in some systems. Modifying nutrient profiles through alterations to land or water use may be a viable alternative for golden alga control in reservoirs. The main objective of this study was to improve our understanding of the nutrient dynamics that influence golden alga bloom formation and toxicity in west Texas reservoirs. We examined eight sites in the Upper Colorado River basin, Texas: three impacted reservoirs that have experienced repeated golden alga blooms; two reference reservoirs where golden alga is present but nontoxic; and three confluence sites downstream of the impacted and reference sites. Total, inorganic, and organic nitrogen and phosphorus and their ratios were quantified monthly along with golden alga abundance and ichthyotoxicity between December 2010 and July 2011. Blooms persisted for several months at the impacted sites, which were characterized by high organic nitrogen and low inorganic nitrogen. At impacted sites, abundance was positively associated with inorganic phosphorus and bloom termination coincided with increases in inorganic nitrogen and decreases in inorganic phosphorus in late spring. Management of both inorganic and organic forms of nutrients may create conditions in reservoirs unfavorable to golden alga.

Journal of the American Water Resources Associatio

Associations between water physicochemistry and Prymnesium parvum presence, abundance, and toxicity in west Texas reservoirs

Toxic blooms of golden alga ( Prymnesium parvum ) have caused substantial ecological and economic harm in freshwater and marine systems throughout the world. In North America, toxic blooms have impacted freshwater systems including large reservoirs. Management of water chemistry is one proposed option for golden alga control in these systems. The main objective of this study was to assess physicochemical characteristics of water that influence golden alga presence, abundance, and toxicity in the Upper Colorado River basin (UCR) in Texas. The UCR contains reservoirs that have experienced repeated blooms and other reservoirs where golden alga is present but has not been toxic. We quantified golden alga abundance (hemocytometer counts), ichthyotoxicity (bioassay), and water chemistry (surface grab samples) at three impacted reservoirs on the Colorado River; two reference reservoirs on the Concho River; and three sites at the confluence of these rivers. Sampling occurred monthly from January 2010 to July 2011. Impacted sites were characterized by higher specific conductance, calcium and magnesium hardness, and fluoride than reference and confluence sites. At impacted sites, golden alga abundance and toxicity were positively associated with salinity-related variables and blooms peaked at ~10°C and generally did not occur above 20°C. Overall, these findings suggest management of land and water use to reduce hardness or salinity could produce unfavorable conditions for golden alga.

Journal of the American Water Resources Associatio

Reproductive biology of invasive grass carp (Ctenopharyngodon idella) in two North American systems

Grass carp ( Ctenopharyngodon idella ) are nonnative, herbivorous freshwater fish that represent an ecological threat in North American waters. However, data are limited on reproductive biology specific to wild populations in midwestern North America, despite recent concern for grass carp establishment within the Great Lakes. Basic information on reproductive traits could be useful to determine reproductive potential, inform future population modelling and provide information to aid control efforts. Our objectives were to evaluate grass carp age-at-maturity, spawning season timing, fecundity type, developmental timing and spawning strategy. Additionally, we evaluated the reliability of the gonadosomatic index (GSI) as a proxy for identifying mature grass carp and compared body condition across study areas. We sampled grass carp in portions of the Mississippi River watershed within the state of Missouri and within the Lake Erie basin. Based on gonad histological samples ( n = 274), grass carp are batch spawners with indeterminate fecundity and asynchronous ovarian developmental timing. This allows flexibility in their spawning, exemplified by a protracted spawning season in Lake Erie (April to November) in temperatures ranging from 12.3 to 27.3°C. Minimum observed age-at-maturity for females in Missouri and for both males and females in the Lake Erie population was age-3 and age-2 for males in Missouri. Accuracy of GSI as a measure of maturity during the spawning season was 89.7% and 87.5%, for females and males, respectively. Compared to Missouri, grass carp in Lake Erie had a significantly higher body condition, and females ready to spawn had significantly higher GSI values, suggesting that the grass carp in Lake Erie are healthier and more fecund relative to Missouri and, if left uncontrolled, potentially have a high probability of establishment within the Great Lakes. The results of this study will allow managers to identify the reproductive status of grass carp in the field and more accurately estimate populations and reproductive potential.

Michigan, Missouri, Ohio

Trout in hot water: A call for global action

Trout are one of the most culturally, economically, and ecologically important taxonomic groups of freshwater fishes worldwide (1). Native to all continents in the Northern Hemisphere, trout are a taxonomically diverse group of fishes belonging to 7 genera (Oncorhynchus, Salvelinus, Salmo, Hucho, Parahucho, Brachymystax, and Salvethymus) distributed across 52 countries. These coldwater specialists provide recreation and food to millions of people, and play important roles in ecosystem functioning and health (2). They are also extremely sensitive to human disturbances because they require cold, clean, complex, and connected habitats for survival and persistence (3) – all attributes that humans have substantially altered and degraded (4, 5). Despite their broad importance as societal icons and as indicators of biodiversity, many of the world’s trout species and lineages are endangered and some require immediate conservation efforts to reverse their precarious decline.

Science