Tropical estuarine ecosystem change under the interacting influences of future climate and ecosystem restoration

One of the largest restoration programs in the world, the Comprehensive Everglades Restoration Plan (CERP) aims to restore freshwater inputs to Everglades wetlands and the Florida Bay estuary. This study predicted how the Florida Bay ecosystem may respond to hydrological restoration from CERP within the context of contemporary projected impacts of sea-level rise (SLR) and increased future temperatures. A spatial–temporal dynamic model (Ecospace) was used to develop a spatiotemporal food web model incorporating environmental drivers of salinity, salinity variation, temperature, depth, distance to mangrove, and seagrass abundance and was used to predict responses of biomass, fisheries catch, and ecosystem resilience between current and future conditions. Changes in biomass between the current and future scenario suggest a suite of winners and losers, with many estuarine species increasing in both total biomass and spatial distribution. Notable biomass increases were predicted for important forage species, including bay anchovy (+32%), hardhead halfbeak (+19%), and pinfish (+31%), while decreases were predicted in mullet (−88%), clupeids (−55%), hardhead silverside (−15%), mojarras (−117%), and Portunid crabs (−16%). Increases in sportfish biomass included the angler-preferred spotted seatrout (+9%), red drum (+10%), and gray snapper (+8%), while decreases included sheepshead (−40%), Atlantic tarpon (−73%), and common snook (−507%). Ecosystem resilience and fisheries catch of angler-preferred species were predicted to improve in the future scenario in total, although a localized decline in resilience predicted for the Central Region may warrant further attention. Our results suggest the Florida Bay ecosystem is likely to achieve restoration benefits in spite of, and in some cases facilitated by, the projected future impacts from climate change due to the system's shallow depth and detrital dominance. The incorporation of climate impacts into long-term restoration planning using ecosystem modeling in similar systems facing unknown futures of SLR, warming seas, and shifting species distributions is recommended.     

Upper Mississippi River restoration: implementation,monitoring, and learning since 1986

Upper Mississippi River Restoration (UMRR) was implemented to monitor environmental status and trends and restore degraded habitat. There was little experience conducting restoration in large rivers, and engineering and ecological integration evolved through project implementation. Loss of depth in backwaters and side channels, excessive biological oxygen demand, increased currents, and low water temperatures were common symptoms of backwater eutrophication that were primary objectives for implementing UMRR. Biological outcome monitoring was initially funded for six projects using the most common methods to restore aquatic and wetland habitat. UMRR island construction occurred as four generations of learning. Current plans represent a comprehensive restoration approach including: physical process modeling (i.e. hydraulic and wind‐wave modeling) of existing conditions and alternative restoration measures. Habitat Rehabilitation and Enhancement Projects, fish response monitoring validated winter habitat suitability models. Long term fish population monitoring indicates sustainable recovery, and now population interaction among restored lakes is under investigation. Isolated wetland management in Illinois River backwater lakes can achieve bottom consolidation that promotes emergent wetland habitat response that migratory waterfowl exploit in large numbers. Adult fish movement between the river and management units is restricted to flood stage or through control structures and post‐project movements into the lake for overwintering were not apparent. The lack of Illinois River overwintering habitat is shown by an abundance of young fish and few older fish in status and trends monitoring. Upper Mississippi River System ecosystem restoration practitioners have implemented ecosystem restoration science and practice in a manner that exemplifies the best intent of adaptive management.     

Effects of Flow Restoration and Exotic Species Removal on Recovery of Native Fish: Lessons from a Dam Decommissioning

Flow diversion and invasive species are two major threats to freshwater ecosystems, threats that restoration efforts attempt to redress. Yet, few restoration projects monitor whether removal of these threats improve target characteristics of the ecosystem. Fewer still have an appropriate experimental design from which causal inferences can be drawn as to the relative merits of removing exotic fish, restoring flow, or both. We used a dam decommissioning in Fossil Creek, Arizona, to compare responses of native fish to exotic fish removal and flow restoration, using a before‐after‐control‐impact design with three impact treatments: flow restoration alone where exotics had not been present, flow restoration and exotic fish removal, and flow restoration where exotics remain and a control reach that was unaffected by restoration actions. We show that removal of exotic fish dramatically increased native fish abundance. Flow restoration also increased native fish abundance, but the effect was smaller than that from removing exotics. Flow restoration had no effect where exotic fish remained, although it may have had other benefits to the ecosystem. The cost to restore flow ($12 million) was considerably higher than that to eradicate exotics ($1.1 million). The long‐term influence of flow restoration could increase, as travertine dams grow and re‐shape the creek increasing habitat for native fish. But in the 2‐year period considered here, the return on investment for extirpating exotics far exceeded that from flow restoration. Projects aimed to restore native fish by restoring flow should also consider the additional investment required to eradicate exotic fish.     

Depth gradients in food‐web processes linking habitats in large lakes: Lake Superior as an exemplar ecosystem

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Contrasting Functional Performance of Juvenile Salmon Habitat in Recovering Wetlands of the Salmon River Estuary, Oregon, U.S.A.

For an estuarine restoration project to be successful it must reverse anthropogenic effects and restore lost ecosystem functions. Restoration projects that aim to rehabilitate endangered species populations make project success even more important, because if misjudged damage to already weakened populations may result. Determining project success depends on our ability to assess the functional state or “performance” and the trajectory of ecosystem development. Mature system structure is often the desired “end point” of restoration and is assumed to provide maximum benefit for target species; however, few studies have measured linkages between structure and function and possible benefits available from early recovery stages. The Salmon River estuary, Oregon, U.S.A., offers a unique opportunity to simultaneously evaluate several estuarine restoration projects and the response of the marsh community while making comparisons with a concurring undiked portion of the estuary. Dikes installed in three locations in the estuary during the early 1960s were removed in 1978, 1987, and 1996, creating a “space‐for‐time substitution” chronosequence. Analysis of the marsh community responses enables us to use the development state of the three recovering marshes to determine a trajectory of estuarine recovery over 23 years and to make comparisons with a reference marsh. We assessed the rate and pattern of juvenile salmon habitat development in terms of fish density, available prey resources, and diet composition of wild juvenile Oncorhynchus tshawytscha (chinook salmon). Results from the outmigration of 1998 and 1999 show differences in fish densities, prey resources, and diet composition among the four sites. Peaks in chinook salmon densities were greatest in the reference site in 1998 and in the youngest (1996) site in 1999. The 1996 marsh had higher densities of chironomids (insects; average 864/m²) and lower densities of amphipods (crustaceans; average 8/m³) when compared with the other sites. Fauna differences were reflected in the diets of juvenile chinook with those occupying the 1978 and 1996 marshes based on insects (especially chironomids), whereas those from the 1987 and reference marshes were based on crustaceans (especially amphipods). Tracking the development of recovering emergent marsh ecosystems in the Salmon River estuary reveals significant fish and invertebrate response in the first 2 to 3 years after marsh restoration. This pulse of productivity in newly restored systems is part of the trajectory of development and indicates some level of early functionality and the efficacy of restoring estuarine marshes for juvenile salmon habitat. However, to truly know the benefits consumers experience in recovering systems requires further analysis that we will present in forthcoming publications.     

Top‐Down Control of Reed Detritus Processing in a Lake Littoral Zone: Experimental Evidence of a Seasonal Compensation between Fish and Invertebrate Predation

We investigated whether predatory fish exert a top‐down control on reed leaf packs processing in a lake littoral zone through a trophic cascade. Exclosure experiments were repeated in summer and winter, under high and low natural fish abundance, respectively. Fish exclusion effects on detritus processing and fungal conditioning were consistent with trophic cascade predictions only in summer. In winter, however, results indicated that a trophic cascade was induced by predatory invertebrates. In both seasons, variations in detritivores abundance generally supported a cascade scenario, whereas several taxon‐specific departures occurred during the experimental periods. We conclude suggesting that predators may continuously regulate leaf detritus processing in lake littoral zones, through a seasonal shift in the relative contribution of fish and invertebrate predation. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Characterization of the mesophotic reef fish community in south Florida,USA

The southeastern coast of Florida, USA supports a substantial recreational fishery, yet little is known of the coral reef ecosystem or fisheries resources past 50 m depth. Fish assemblages associated with low‐relief substrate and three vessel reefs between 50 and 120 m depth off southeast Florida were surveyed by remotely operated vehicles providing the first characterization of the mesophotic fish assemblages in the region. Two distinct assemblages were observed on low‐relief substrate and high‐relief vessel reefs. A total of 560 fishes of 42 species was recorded on 27 dives on low‐relief substrate, and 50 152 fishes of 65 species were recorded on 24 dives on three vessel reefs. Small planktivorous Anthiinae fishes and several economically valuable species were common on vessel reefs but rare on low‐relief substrate. Fish assemblages on vessel reefs more closely resembled those found at similar depths in high‐relief natural areas off east‐central Florida and the Gulf of Mexico than those associated with adjacent low‐relief habitat or nearby coral reef tracts. From a fisheries perspective, these results provide limited support to the hypothesis that in deep‐water regions with limited relief, vessel reefs may provide an opportunity to increase fish diversity and abundance by creating high‐relief habitat without compromising adjacent fish assemblages.     

Comparing the recovery of richness,structure, and biomass in naturally regrowing and planted reforestation

The clearing of natural vegetation for agriculture has reduced the capacity of natural systems to provide ecosystem functions. Ecological restoration can restore desirable ecosystem functions, such as creating habitat for animal conservation and carbon sequestration as woody biomass. In order to maintain these beneficial ecosystem functions, restoration projects need to mature into self‐perpetuating communities. Here we compared the ecological attributes of two types of restoration, “active” tree plantings with “passive” natural forest regeneration (“natural regrowth”) to existing remnant vegetation in a cleared agricultural landscape. Specifically, we measured differences between forest categories in factors that may predict future restoration failure or ecosystem collapse: aboveground plant biomass and biomass accrual over time (for regrowing stands), plant density and size class distributions, and diversity of functional groups based on seed dispersal and growth strategy traits. We found that natural regrowth and planted forests were similar in many ecological characteristics, including biomass accrual. Despite this, planted stands contained fewer tree recruit and shrub individuals, which may be due to limited recruitment in plantings. If this continues, these forests may be at risk of collapsing into nonforest states after mature trees senesce. Lower shrub density and richness of mid‐story trees may lead to lower structural complexity in planting plots, and alongside lower richness of fleshy‐fruited plant species may reduce animal resources and animal use of the restored stand. In our study region, natural regrowth may result in restored woodland communities with greater conservation and carbon mitigation value.     

Near‐term impacts of coral restoration on target species,coral reef community structure,and ecological processes

The global decline of corals has created an urgent need for effective, science‐based methods to augment coral populations and restore important ecosystem functions. To meet this challenge, the field of coral restoration has rapidly evolved over the past decade. However, despite widespread efforts to outplant corals and monitor survivorship, there is a shortage of information on the effects of coral restoration on reef communities or important ecosystem functions. To fill this knowledge gap, we examined the effects of restoration on three major criteria: diversity, community structure, and ecological processes. We conducted surveys of four restored sites in the Florida Keys ranging in restoration effort (500–2,300 corals outplanted) paired with surveys of nearby, unmanipulated control sites. Coral restoration successfully enhanced coral populations, increasing coral cover 4‐fold, but manifested in limited differences in coral and fish communities. Some restored sites had higher abundance of herbivorous fish, rates of herbivory, or more juvenile‐sized corals, but these effects were limited to individual reefs. Damselfish were consistently more abundant at restored compared to control sites. Despite augmenting target coral populations, 3 years of coral restoration has not facilitated many of the positive feedbacks that help reinforce coral success. In a time of increasingly frequent disturbances, it is urgent we hasten the speed at which reefs recover important ecological processes, such as herbivory and nutrient cycling, that make reefs more resistant and resilient if we are to achieve long‐term restoration success.     

Linking fish trait responses to in‐stream habitat in reconstructed valley‐plugged stream reaches of the Coastal Plain,U.S.A.

Valley‐plug formation is a challenging consequence of stream channelization especially in physiographic regions with highly erodible soils. Upstream channel degradation and incision results in accelerated sediment delivery processes wherein downstream aggradation decreases stream power and creates sand‐clogged channels. Channel reconstruction is now meeting hydrogeomorphic goals related to valley‐plug remediation, yet there exists a need to understand how this practice also facilitates ecological restoration. We evaluated fish trait response to in‐stream habitat conditions in channelized, recently restored, and “least‐disturbed” reference reaches of Coastal Plain streams in West Tennessee. Restored reaches were ecologically similar to channelized reaches, having higher proportions of nest‐guarding omnivores that were correlated with higher percentages of pool habitats and lower wetted width:depth ratios compared to reference reaches. Reference reaches had higher proportions of fast‐water dwelling and specialized insectivores that were correlated with high abundance of large woody debris, high‐wetted width:depth ratios, and low percentages of pool habitats. We conclude that in‐stream habitats in reconstructed channels have yet to promote reach‐scale ecological restoration relative to fish assemblage organization because trait‐habitat associations were not similar to reference conditions. However, our results lend to the development of ecological restoration targets that can be incorporated in future channel reconstruction projects in valley‐plugged, channelized streams of the Coastal Plain.     

Recovery of mammal diversity in tropical forests: a functional approach to measuring restoration

Ecological restoration is increasingly applied in tropical forests to mitigate biodiversity loss and recover ecosystem functions. In restoration ecology, functional richness, rather than species richness, often determines community assembly, and measures of functional diversity provide a mechanistic link between diversity and ecological functioning of restored habitat. Vertebrate animals are important for ecosystem functioning. Here, we examine the functional diversity of small‐to‐medium sized mammals to evaluate the diversity and functional recovery of tropical rainforest. We assess how mammal species diversity and composition and functional diversity and composition, vary along a restoration chronosequence from degraded pasture to “old‐growth” tropical rainforest in the Wet Tropics of Australia. Species richness, diversity, evenness, and abundance did not vary, but total mammal biomass and mean species body mass increased with restoration age. Species composition in restoration forests converged on the composition of old‐growth rainforest and diverged from pasture with increasing restoration age. Functional metrics provided a clearer pattern of recovery than traditional species metrics, with most functional metrics significantly increasing with restoration age when taxonomic‐based metrics did not. Functional evenness and dispersion increased significantly with restoration age, suggesting that niche complementarity enhances species' abundances in restored sites. The change in community composition represented a functional shift from invasive, herbivorous, terrestrial habitat generalists and open environment specialists in pasture and young restoration sites, to predominantly endemic, folivorous, arboreal, and fossorial forest species in older restoration sites. This shift has positive implications for conservation and demonstrates the potential of tropical forest restoration to recover rainforest‐like, diverse faunal communities.     

Changes in habitat availability for outmigrating juvenile salmon (Oncorhynchus spp.) following estuary restoration

The restoration of the Nisqually River Delta (Washington, U.S.A.) represents one of the largest efforts toward reestablishing the ecosystem function and resilience of modified habitat in the Puget Sound, particularly for anadromous salmonid species. The opportunity for outmigrating salmon to access and benefit from the expansion of available tidal habitat can be quantified by several physical attributes, which are related to the ecological and physiological responses of juvenile salmon. We monitored a variety of physical parameters to measure changes in opportunity potential from historic, pre‐restoration, and post‐restoration habitat conditions at several sites across the delta. These parameters included channel morphology, water quality, tidal elevation, and landscape connectivity. We conducted fish catch surveys across the delta to determine if salmon was utilizing restored estuary habitat. Overall major channel area increased 42% and major channel length increased 131% from pre‐ to post‐restoration conditions. Furthermore, the results of our tidal inundation model indicated that major channels were accessible up to 75% of the time, as opposed to 30% pre‐restoration. Outmigrating salmon utilized this newly accessible habitat as quickly as 1 year post‐restoration. The presence of salmon in restored tidal channels confirmed rapid post‐restoration increases in opportunity potential on the delta despite habitat quality differences between restored and reference sites.     

When is translocation required for the population recovery of old‐growth epiphytes in a reforested landscape?

It is often assumed that species recolonization follows from the restoration of key habitat structure. Thus, forest restoration focuses on the recovery of trees into deforested landscapes, so that a multitude of associated organisms can achieve “colonization credit” and recolonize from remnant source populations into restored habitat. This opportunity for recolonization exists because species vulnerable to habitat loss may experience an “extinction debt,” during which their remnant populations decline only slowly to equilibrium with a deforested landscape. These persistent but declining populations become propagule sources for recolonization. To test limits to “colonization credit,” this study focused on old‐growth dependent lichen epiphytes, using a simulation to identify a hypothetical threshold at which: (1) the number of remnant populations, and (2) their population sizes, are too low to achieve recolonization and population recovery, despite efforts placed into forest restoration. The results show that for a landscape scenario relevant to the industrialized temperate zone, with less than 5% of old‐growth forest remaining, and ambitions for restoration to circa 10–15% forest cover, there is a failure to achieve population recovery over long timescales (i.e. within 600 years), making translocation a necessary option. This delay represents a “colonization deficit” that may be a common feature in ecological restoration more generally.     

Sustainability of the Lake Superior Fish Community: Interactions in a Food Web Context

The restoration and rehabilitation of the native fish communities is a long-term goal for the Laurentian Great Lakes. In Lake Superior, the ongoing restoration of the native lake trout populations is now regarded as one of the major success stories in fisheries management. However, populations of the deepwater morphotype (siscowet lake trout) have increased much more substantially than those of the nearshore morphotype (lean lake trout), and the ecosystem now contains an assemblage of exotic species such as sea lamprey, rainbow smelt, and Pacific salmon (chinook, coho, and steelhead). Those species play an important role in defining the constraints and opportunities for ecosystem management. We combined an equilibrium mass balance model (Ecopath) with a dynamic food web model (Ecosim) to evaluate the ecological consequences of future alternative management strategies and the interaction of two different sets of life history characteristics for fishes at the top of the food web. Relatively rapid turnover rates occur among the exotic forage fish, rainbow smelt, and its primary predators, exotic Pacific salmonids. Slower turnover rates occur among the native lake trout and burbot and their primary prey—lake herring, smelt, deepwater cisco, and sculpins. The abundance of forage fish is a key constraint for all salmonids in Lake Superior. Smelt and Mysis play a prominent role in sustaining the current trophic structure. Competition between the native lake trout and the exotic salmonids is asymmetric. Reductions in the salmon population yield only a modest benefit for the stocks of lake trout, whereas increased fishing of lake trout produces substantial potential increases in the yields of Pacific salmon to recreational fisheries. The deepwater or siscowet morphotype of lake trout has become very abundant. Although it plays a major role in the structure of the food web it offers little potential for the restoration of a valuable commercial or recreational fishery. Even if a combination of strong management actions is implemented, the populations of lean (nearshore) lake trout cannot be restored to pre-fishery and pre-lamprey levels. Thus, management strategy must accept the ecological constraints due in part to the presence of exotics and choose alternatives that sustain public interest in the resources while continuing the gradual progress toward restoration. Received 10 December 1999; accepted 13 June 2000.     

Littoral habitat loss caused by multiyear drought and the response of an endemic fish species in a deep desert lake

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Stocked trout have minimal effects on littoral invertebrate assemblages of productive fish‐bearing lakes: a whole‐lake BACI study

1. Rainbow Trout (Oncorhynchus mykiss [Walbaum]) is commonly stocked as a sport fish throughout the world but can have serious negative effects on native species, especially in headwater systems. Productive fish‐bearing lakes represent a frequently stocked yet infrequently studied system, and effects of trout in these systems may differ from those in headwater lakes. 2. We used a Before‐After Control‐Impact (BACI) design to determine how stocked trout affected assemblage‐level and taxon‐level biomass, abundance and average length of littoral invertebrates in a stocked lake relative to three unstocked control lakes in the boreal foothills of Alberta, Canada. Lakes were studied 1 year before and for 2 years after stocking. Because characteristics of productive fish‐bearing lakes should buffer impacts of introduced fish, we predicted that trout would not affect assemblage‐level structure of littoral invertebrates but might reduce the abundance or average length of large‐bodied taxa frequently consumed by trout. 3. Relative to the unstocked control lakes, biomass, but not abundance, of the littoral invertebrate assemblage was affected indirectly by trout through increases of some taxa after trout stocking. At the individual taxon‐level, trout stocking did not affect most (23 of the 27) taxa, with four taxa increasing in abundance or biomass after stocking. Only one taxon, Chironomidae, showed evidence of size‐selective predation by trout, being consumed frequently by trout and decreasing significantly in average length after stocking. 4. Our results contrast with the strong negative effects of trout stocking on invertebrate assemblages commonly reported from headwater lakes. A combination of factors, including large and robust native populations of forage fish, the generalised diet of trout, overwinter aeration, relatively high productivity and dense macrophyte beds, likely works in concert to reduce potentially negative effects of stocked trout in these systems. As such, productive, fish‐bearing lakes may represent a suitable system for trout stocking, especially where native sport fish populations are lacking.     

Edge effects influence the composition and density of reef residents on subtidal restored oyster reefs

Within estuarine and coastal ecosystems globally, extensive habitat degradation and loss threaten critical ecosystem functions and necessitate widescale restoration efforts. There is abundant evidence that ecological processes and species interactions can vary with habitat characteristics, which has important implications for the design and implementation of restoration efforts aimed at enhancing specific ecosystem functions and services. We conducted an experiment examining how habitat characteristics (presence; edge vs. interior) influence the communities of resident fish and mobile invertebrates on restored oyster (Crassostrea virginica) reefs. Similar to previous studies, we found that restored reefs altered community composition and augmented total abundance and biomass relative to unstructured sand habitat. Community composition and biomass also differed between the edge and interior of individual reefs as a result of species-specific patterns over small spatial scales. These patterns were only weakly linked to oyster density, suggesting that other factors that vary between edge and interior (e.g. predator access or species interactions) are likely more important for community structure on oyster reefs. Fine-scale information on resident species' use of oyster reefs will help facilitate restoration by allowing decision makers to optimize the amount of edge versus interior habitat. To improve the prediction of faunal use and benefits from habitat restoration, we recommend investigations into the mechanisms shaping edge and interior preferences on oyster reefs.     

Top-down and bottom-up impacts of juvenile fish in a littoral reed stand

1. Research has often focused on pelagic food chains and processes of lakes; less is known about the contribution of benthic energy flows to whole‐lake ecosystem energetics. This stems from the fact that the shoreline and littoral habitats, which provide a key linkage between sediment and water column, have only recently become a significant focus for study. 2. This study aimed to quantify the feeding and phosphorus allocation of a juvenile fish community in a littoral zone of a shallow lake in response to the biomass succession of the invertebrate prey community. Habitats comprising reed and adjacent open water were sampled over two consecutive years during day and night. 3. Although there were substantial year‐to‐year differences in the biomass of invertebrates, the fish community composition, diet consumption rates and phosphorus allocations were very similar in both study years. Biomasses and predation impacts by juvenile fish on prey groups were substantially higher within the reeds than in the adjacent open water habitat. This may be explained by the refuge‐seeking behaviour of the fish. 4. In general, invertebrates were negligibly influenced by fish feeding, with the exception for a strong top‐down control of large cladocerans. In response to the resulting low Daphnia biomass, fish were forced to switch to a higher degree of benthivory. Consequently, juvenile fish in littoral reed stands may shift benthic‐derived energy and phosphorus via the excretion of soluble reactive phosphorus into the open water.     

A scientific basis for restoring fish spawning habitat in the St. Clair and Detroit Rivers of the Laurentian Great Lakes

Loss of functional habitat in riverine systems is a global fisheries issue. Few studies, however, describe the decision‐making approach taken to abate loss of fish spawning habitat. Numerous habitat restoration efforts are underway and documentation of successful restoration techniques for spawning habitat of desirable fish species in large rivers connecting the Laurentian Great Lakes are reported here. In 2003, to compensate for the loss of fish spawning habitat in the St. Clair and Detroit Rivers that connect the Great Lakes Huron and Erie, an international partnership of state, federal, and academic scientists began restoring fish spawning habitat in both of these rivers. Using an adaptive management approach, we created 1,100 m² of productive fish spawning habitat near Belle Isle in the Detroit River in 2004; 3,300 m² of fish spawning habitat near Fighting Island in the Detroit River in 2008; and 4,000 m² of fish spawning habitat in the Middle Channel of the St. Clair River in 2012. Here, we describe the adaptive‐feedback management approach that we used to guide our decision making during all phases of spawning habitat restoration, including problem identification, team building, hypothesis development, strategy development, prioritization of physical and biological imperatives, project implementation, habitat construction, monitoring of fish use of the constructed spawning habitats, and communication of research results. Numerous scientific and economic lessons learned from 10 years of planning, building, and assessing fish use of these three fish spawning habitat restoration projects are summarized in this article.     

Larval fish assemblage recovery: a reflection of environmental change in a large degraded river

Estuaries are globally important to fisheries but face many anthropogenic stressors that reduce water quality and degrade benthic habitat. The Maumee River estuary has been degraded by industrial contaminants, high sediment and nutrient loads, channelization and elimination of surrounding wetlands, lessening its value as spawning habitat for fishes of Lake Erie. Regulation and better management practices (BMPs) in the watershed have improved the water quality in this estuary, which should result in a response of the biotic community. We compared recent (2010/2011) larval fish assemblage data to similar data from the 1970s (1976/1977) in order to identify changes due to improved water and habitat quality. Family‐level diversity was greater in recent study years compared to the 1970s and family richness increased from 6 to 10. In addition, the abundance of lithophilic spawning fishes was significantly greater in the recent study years. Increased diversity and family richness were consistent with increased water quality in the Maumee River whereas the observed increase in abundance of lithophilic spawners was consistent with an increase in the amount or quality of benthic habitat used by species in these families for spawning. Better wastewater management and agricultural practices in coastal watersheds can benefit the early life stages of fishes, thus benefitting coastal fisheries. Furthermore, larval fish assemblages may be useful indicators of biological integrity because of their sensitivities to environmental change. Routine sampling of estuarine larval fish assemblages could provide practitioners with insight into ecosystem changes and measure the response of the biotic community to restoration.