Artificial reefs concentrate nutrients and alter benthic community structure in an oligotrophic, subtropical estuary

The construction of artificial reefs in the oligotrophic seagrass meadows of central Florida Bay attracted large aggregations of fish and invertebrates, and assays of nutrient availability indicated increases in availability of nutrients to sediment microalgae, periphyton, and seagrasses around reefs. An average of 37.8 large (> 10 cm) mobile animals were observed on each small artificial reef. The dominant fish species present was the gray snapper (Lutjanus griseus Linnaeus, 1758). Four yrs after the establishment of the artificial reefs, microphytobenthos abundance was twice as high in reef plots (1.7 ± 0.1 μg chl-a cm-2) compared to control plots (0.9 ± 0.1 μg chl-a cm-2). The accumulation of periphyton on glass periphytometers was four times higher in artificial reef plots (200.1 ± 45.8 mg chl-a m-2) compared to control plots (54.8 ± 6.8 mg chl-a m-2). The seagrass beds surrounding the artificial reefs changed rapidly, from a sparse Thalassia testudinum (Banks & Soland. ex König) dominated community, which persisted at control plots, to a community dominated by Halodule wrightii (Ascherson). Such changes mirror the changes induced in experimentally fertilized seagrass beds in Florida, strongly suggesting that the aggregations of animals attracted by artificial reefs concentrated nutrients in this oligotrophic seascape, favoring the growth of fast-growing primary producers like microphytobenthos and periphyton, and changing the competitively dominant seagrass from slow-growing T. testudinum to faster-growing H. wrightii in the vicinity of the reefs.

Comparison of community structure of mangrove and riprap rock habitats along urban coastlines of south Florida

Globally, mangrove ecosystems have substantially declined, largely a result of human impacts. Mangroves provide a number of ecosystem services such as shoreline stabilization and nursery habitat for fish species. As declines continue, many of these ecosystem services are lost or altered. The need for shoreline stabilization has become increasingly apparent when chronic erosion wear away coastlines once mangroves are removed. Limestone boulders called riprap have been employed to offset continued erosion associated with mangrove clearing. In urban coastal areas adjacent to Biscayne Bay, Florida, as much as 80 percent of mangroves have been lost. More recently, riprap has been used in conjunction with mangroves to restore wetlands throughout the Bay. This riprap-mangrove habitat provides structure for marine organisms to colonize. However, fish assemblages and benthic composition could vary between this hybridized habitat and natural mangrove systems. Comparisons of fish and benthic community structure were made, to determine if abundance, species richness, and overall diversity differed between the two habitat types. Visual census and benthic quadrat surveys were conducted in vi mangrove and mangrove-riprap sites within two regions of Biscayne Bay. Total fish abundance was greater in mangroves, but the effect of habitat type on species richness varied between regions. The community structure of fishes and benthic composition differed significantly between mangroves and riprap habitats. Because species composition is so distinct, it is likely that the two communities do no function in the same manner. In areas with cleared shorelines, it may be important to consider the function of added anthropogenic structure for ecological communities.

Novel methodology for in situ carbon dioxide enrichment of benthic ecosystems

Future climate change will likely represent a major stress to shallow aquatic and coastal marine communities around the world. Most climate change research, particularly in regards to increased pCO2 and ocean acidification, relies on ex situ mesocosm experimentation, isolating target organisms from their environment. Such mesocosms allow for greater experimental control of some variables, but can often cause unrealistic changes in a variety of environmental factors, leading to “bottle effects.” Here we present an in situ technique of altering dissolved pCO2within nearshore benthic communities (e.g., macrophytes, algae, and/or corals) using submerged clear, open-top chambers. Our technique utilizes a flow-through design that replicates natural water flow conditions and minimizes caging effects. The clear, open-top design additionally ensures that adequate light reaches the benthic community. Our results show that CO2 concentrations and pH can be successfully manipulated for long durations within the open-top chambers, continuously replicating forecasts for the year 2100. Enriched chambers displayed an average 0.46 unit reduction in pH as compared with ambient chambers over a 6-month period. Additionally, CO2 and HCO3 – concentrations were all significantly higher within the enriched chambers. We discuss the advantages and disadvantages of this technique in comparison to other ex situ mesocosm designs used for climate change research.

Disturbance regime and limits on benefits of refuge use for fishes in a fluctuating hydroscape

Refuge habitats increase survival rate and recovery time of populations experiencing environmental disturbance, but limits on the ability of refuges to buffer communities are poorly understood. We hypothesized that importance of refuges in preventing population declines and alteration in community structure has a non-linear relationship with severity of disturbance. In the Florida Everglades, alligator ponds are used as refuge habitat by fishes during seasonal drying of marsh habitats. Using an 11-year record of hydrological conditions and fish abundance in 10 marshes and 34 alligator ponds from two regions of the Everglades, we sought to characterize patterns of refuge use and temporal dynamics of fish abundance and community structure across changing intensity, duration, and frequency of drought disturbance. Abundance in alligator ponds was positively related to refuge size, distance from alternative refugia (e.g. canals), and abundance in surrounding marsh prior to hydrologic disturbance. Variables negatively related to abundance in alligator ponds included water level in surrounding marsh and abundance of disturbance-tolerant species. Refuge community structure did not differ between regions because the same subset of species in both regions used alligator ponds during droughts. When time between disturbances was short, fish abundance declined in marshes, and in the region with the most spatially extensive pattern of disturbance, community structure was altered in both marshes and alligator ponds because of an increased proportion of species more resistant to disturbance. These changes in community structure were associated with increases in both duration and frequency of hydrologic disturbance. Use of refuge habitat had a modal relationship with severity of disturbance regime. Spatial patterns of response suggest that decline in refuge use was because of decreased effectiveness of refuge habitat in reducing mortality and providing sufficient time for recovery for fish communities experiencing reduced time between disturbance events.

Simulating Mechanisms for Dispersal, Production and Stranding of Small Forage Fish in Temporary Wetland Habitats

Movement strategies of small forage fish (<8 cm total length) between temporary and permanent wetland habitats affect their overall population growth and biomass concentrations, i.e., availability to predators. These fish are often the key energy link between primary producers and top predators, such as wading birds, which require high concentrations of stranded fish in accessible depths. Expansion and contraction of seasonal wetlands induce a sequential alternation between rapid biomass growth and concentration, creating the conditions for local stranding of small fish as they move in response to varying water levels. To better understand how landscape topography, hydrology, and fish behavior interact to create high densities of stranded fish, we first simulated population dynamics of small fish, within a dynamic food web, with different traits for movement strategy and growth rate, across an artificial, spatially explicit, heterogeneous, two-dimensional marsh slough landscape, using hydrologic variability as the driver for movement. Model output showed that fish with the highest tendency to invade newly flooded marsh areas built up the largest populations over long time periods with stable hydrologic patterns. A higher probability to become stranded had negative effects on long-term population size, and offset the contribution of that species to stranded biomass. The model was next applied to the topography of a 10 km × 10 km area of Everglades landscape. The details of the topography were highly important in channeling fish movements and creating spatiotemporal patterns of fish movement and stranding. This output provides data that can be compared in the future with observed locations of fish biomass concentrations, or such surrogates as phosphorus ‘hotspots’ in the marsh.

Biogeochemical Classification of South Florida’s Estuarine and Coastal Waters of Tropical Seagrasses

South Florida’s watersheds have endured a century of urban and agricultural development and disruption of their hydrology. Spatial characterization of South Florida’s estuarine and coastal waters is important to Everglades’ restoration programs. We applied Factor Analysis and Hierarchical Clustering of water quality data in tandem to characterize and spatially subdivide South Florida’s coastal and estuarine waters. Segmentation rendered forty-four biogeochemically distinct water bodies whose spatial distribution is closely linked to geomorphology, circulation, benthic community pattern, and to water management. This segmentation has been adopted with minor changes by federal and state environmental agencies to derive numeric nutrient criteria.

Habitat use and foraging ecology of a batoid community in Shark Bay, Western Australia

Worldwide declines in populations of large elasmobranchs and the potential cascading effects on marine ecosystems have garnered considerable attention. Far less appreciated are the potential ecological impacts of changes in abundances of small to medium bodied elasmobranchs mesopredators. Crucial to elucidating the role of these elasmobranchs is an understanding of their habitat use and foraging ecology in pristine conditions. I investigated the trophic interactions and factors driving spatiotemporal variation in abundances of elasmobranch mesopredators in the relatively pristine ecosystem of Shark Bay, Australia. First, I describe the species composition and seasonal habitat use patterns of elasmobranch mesopredator on the sandflats of Shark Bay. Juvenile batoids dominated this diverse community and were extremely abundant in nearshore microhabitats during the warm season. Stomach content analysis and stable isotopic analysis revealed that there is a large degree of dietary overlap between common batoid species. Crustaceans, which tend to be found in seagrass habitats, dominated diets. Despite isotopic differences between many species, overlap in isotopic niche space was high and there was some degree of individual specialization. I then, investigated the importance of abiotic (temperature and water depth) and biotic (prey and predator abundance) factors in shaping batoid habitat use. Batoids were most abundant and tended to rest in shallow nearshore waters when temperatures were high. This pattern coincides with periods of large shark abundance suggesting batoids were seeking refuge from predators rather than selecting optimal temperatures. Finally, I used acoustic telemetry to examine batoid residency and diel use of the sandflats. Individual batoids were present on the sandflats during both the warm and cold seasons and throughout the diel cycle, suggesting lower sandflat densities during the cold season were a result of habitat shifts rather than migration out of Shark Bay. Combined, habitat use and dietary results suggest that batoids have the potential to seasonally impact sandflat dynamics through their presence, although foraging may be limited on the sandflats. Interestingly, my results suggest that elasmobranch mesopredators in pristine ecosystems probably are not regulated by food supply and their habitat use patterns and perhaps ecosystem impacts may be influenced by their predators.

Understanding anuran community dynamics in temporary wetlands: The interaction and importance of landscape and biotic processes

The major objective of this study was to determine the relative importance of landscape factors, local abiotic factors, and biotic interactions in influencing tadpole community structure in temporary wetlands. I also examined the influence of agricultural activities in South-central Florida by comparing tadpole communities in native prairie wetlands (a relatively unmodified habitat) at the Kissimmee Prairie Sanctuary (KPS) to tadpole communities in three agriculturally modified habitats found at MacArthur Agro-Ecology Research Center (MAERC). Environmental characteristics were measured in 24 isolated wetlands, and tadpoles were sampled using throw-traps and dipnets during the 1999 wet season (June–October). Landscape characteristics were expected to predominately influence all aspects of community structure because anurans associated with temporary wetland systems are likely to exist as metapopulations. Both landscape characteristics (wetland proximity to nearest woodland and the amount of woodland surrounding the wetland) and biotic interactions (fish predation) had the largest influence on tadpole community structure. Predatory fish influenced tadpole communities more than expected due to the ubiquity of wetlands, lack of topographic relief, and dispersal abilities of several fish species. Differences in tadpole community structure among habitat types were attributed to differences in woodland attributes and susceptibility to fish colonization. Furthermore, agricultural modification of prairie habitats in South-central Florida may benefit amphibian communities, particularly woodland-dwelling species that are unable to coexist with predatory fish. From a conservation standpoint, temporary wetlands proximal to woodland areas and isolated from permanent water sources appear to be most important to amphibians. In addition, the high tadpole densities attained in these wetlands suggest that these wetlands serve as biological hotspots within the landscape, and their benefits extend into the adjacent terrestrial matrix. Further research efforts are needed to quantify the biological productivity of these systems and determine spatial dynamics of anurans in surrounding terrestrial habitats. ^

Defining the role of floating periphyton mats in shaping food-web dynamics in the Florida Everglades

Expansive periphyton mats are a striking characteristic of the Florida Everglades. Floating periphyton mats are home to a diverse macroinvertebrate community dominated by chironomid and ceratopogonid larvae and amphipods that use the mat as both a food resource and refuge from predation. While this periphyton complex functions as a self-organizing system, it also serves as a base for trophic interactions with larger organisms. The purpose of my research was to quantify variation in the macroinvertebrate community inhabiting floating periphyton mats, describe the role of mats in shaping food-web dynamics, and describe how these trophic interactions change with eutrophication. ^ I characterized the macroinvertebrate community inhabiting periphyton through a wet-season by describing spatial variation on scales from 0.2 m to 3 km. Floating periphyton mats contained a diverse macroinvertebrate community, with greater taxonomic richness and higher densities of many taxa than adjacent microhabitats. Macroinvertebrate density increased through the wet season as periphyton mats developed. While some variation was noted among sites, spatial patterns were not observed on smaller scales. I also sampled ten sites representing gradients of hydroperiod and nutrient (P) levels. The density of macroinvertebrates inhabiting periphyton mats increased with increasing P availability; however, short-hydroperiod P-enriched sites had the highest macroinvertebrate density. This pattern suggests a synergistic interaction of top-down and bottom-up effects. In contrast, macroinvertebrate density was lower in benthic floc, where it was negatively correlated with hydroperiod. ^ I used two types of mesocosms (field cages and tanks) to manipulate large consumers (fish and grass shrimp) with inclusion/exclusion cages over an experimental P gradient. In most cases, periphyton mats served as an effective predation refuge. Macroinvertebrates were consumed more frequently in P-enriched treatments, where mats were also heavily grazed. Macroinvertebrate densities decreased with increasing P in benthic floc, but increased with enrichment in periphyton mats until levels were reached that caused disassociation of the mat. ^ This research documents several indirect trophic interactions that can occur in complex habitats, and emphasizes the need to characterize dynamics of all microhabitats to fully describe the dynamics of an ecosystem. ^

Distribution and ecology of amphibians and reptiles in a fragmented landscape, northeastern Bolivia

Habitat loss and fragmentation have been implicated as driving forces behind recent waves of extinction. The regional landscape where this study occurred is a mosaic of forest and grassland, and therefore provides an ideal system with which to investigate the implications of habitat patchiness for the distribution and ecology of organisms. Here I describe patterns of amphibian and reptile distribution among and within habitats at the study site, investigate associations between habitat and community structure, describe nested subset patterns on forest islands, and quantify the relationship between body size and density across ecological scales and taxonomic groups. ^ Species richness did not vary across habitats, between forest island isolation classes or between island edges and cores. In contrast, species composition varied at all three ecological scales, reflecting differences in the distribution of both forest and open-habitat affiliated species. Species composition was associated with multivariate habitat profiles, with differences occurring along the isolation gradient of forest islands rather than the area gradient. The relationship between species composition and habitat was stronger for amphibians than for reptiles, a pattern that may be ascribed to physiological differences between the two groups. Analysis of nested subset pattern of community structure indicated that species composition of islands is nested as a function of isolation. Four species whose distribution on forest islands seems to be dispersal-limited drive the relationship between nestedness and isolation. Although there were several examples of shifts in body size across spatial scales and taxonomic groups, body size was not associated with density as predicted by theory, which may reflect differences between real and habitat islands, or differential responses of poikilothermic vertebrates to changes in density relative to homeotherms. ^ Taken together, the strongest result to emerge from this research is the importance of isolation, rather than area, on community structure in this system. Much evidence suggested that different ecological groups of species show distinct patterns of distribution both within and among habitat types. This suggests that species distributions at this site are not the result of 'neutral' processes at the community level, but rather reflect fundamental differences in the ecology of component species. ^

Relative significance of pelagic, benthic and allochthonous organic matter to microbial carbon cycling in a phosphorus-depleted subtropical estuary (Florida Bay)

Heterotrophic bacteria are important decomposers and transformers of primary production and provide an important link between detritus and the aquatic food web. In seagrass ecosystems, much of seagrass primary production is unavailable through direct grazing and must undergo microbial reworking before seagrass production can enter the aquatic food web. The goal of my dissertation research is to understand better the role heterotrophic bacteria play in carbon cycling in seagrass estuaries. My dissertation research focuses on Florida Bay, a seagrass estuary that has experienced recent changes in carbon source availability, which may have altered ecosystem function. My dissertation research investigates the importance of seagrass, algal and/or cyanobacterial, and allochthonous-derived organic matter to heterotrophic bacteria in Florida Bay and helps establish the carbon base of the estuarine food web. ^ A three tiered approach to the study of heterotrophic bacterial carbon cycling and trophic influences in Florida Bay was used: (1) Spatiotemporal observations of environmental parameters (hydrology, nutrients, extracellular enzymes, and microbial abundance, biomass, and production); (2) Microbial grazing experiments under different levels of top-down and bottom-up influence; and (3) Bulk and compound-specific (bacteria-biomarker fatty acid analysis) stable carbon isotope analysis. ^ In Florida Bay, spatiotemporal patterns in microbial extracellular enzyme (also called ectoenzyme) activities indicate that microorganisms hydrolyzed selectively fractions of the estuarine organic matter pool. The microbial community hydrolyzed organic acids, peptides, and phosphate esters and did not use storage and structural carbohydrates. Organic matter use by heterotrophic bacterioplankton in Florida Bay was co-regulated by bottom-up (resource availability) and top-down (grazer mediated) processes. A bacterial carbon budget based on bacterial, epiphytic, and seagrass production indicates that heterotrophic bacterial carbon cycles are supported primarily through epiphytic production with mixing from seagrass production. Stable carbon isotope analysis of bacteria biomarkers and carbon sources in Florida Bay corroborate the results of the bacterial carbon budget. These results support previous studies of aquatic consumers in Florida Bay, indicating that epiphytic/benthic algal and/or cyanobacterial production with mixing from seagrass-derived organic matter is the carbon base of the seagrass estuarine food web. ^

Ecology and distribution of diatoms in Biscayne Bay, Florida (USA): Implications for bioassessment and paleoenvironmental studies

The spatial and temporal distribution of planktonic, sediment-associated and epiphytic diatoms among 58 sites in Biscayne Bay, Florida was examined in order to identify diatom taxa indicative of different salinity and water quality conditions, geographic locations and habitat types. Assessments were made in contrasting wet and dry seasons in order to develop robust assessment models for salinity and water quality for this region. We found that diatom assemblages differed between nearshore and offshore locations, especially during the wet season when salinity and nutrient gradients were steepest. In the dry season, habitat structure was primary determinant of diatom assemblage composition. Among a suite of physicochemical variables, water depth and sediment total phosphorus (STP) were most strongly associated with diatom assemblage composition in the dry season, while salinity and water total phosphorus (TP) were more important in the wet season. We used indicator species analysis (ISA) to identify taxa that were most abundant and frequent at nearshore and offshore locations, in planktonic, epiphytic and benthic habitats and in contrasting salinity and water quality regimes. Because surface water concentrations of salts, total phosphorus, nitrogen (TN) and organic carbon (TOC) are partly controlled by water management in this region, diatom-based models were produced to infer these variables in modern and retrospective assessments of management-driven changes. Weighted averaging (WA) and weighted averaging partial least squares (WA-PLS) regressions produced reliable estimates of salinity, TP, TN and TOC from diatoms (r2 = 0.92, 0.77, 0.77 and 0.71, respectively). Because of their sensitivity to salinity, nutrient and TOC concentrations diatom assemblages should be useful in developing protective nutrient criteria for estuaries and coastal waters of Florida.

Diel Patterns of Patch Reef Community Dynamics in a Caribbean Back-Reef System

Back-reef seascapes represent critical habitat for juvenile and adult fishes. Patch reef, seagrass, and mangrove habitats form a heterogeneous mosaic, often linked by species that use reefs as structure during the day and make foraging migrations into soft-bottom habitat at night. Artificial reefs are used to model natural patch reefs, however may not function equivalently as fish habitat. To study the relative value of natural and artificial patch reefs as fish habitat, these communities in the Sea of Abaco, Bahamas were compared using roving diver surveys and time-lapse photography. Diel turnover in fish abundance, recorded with time-lapse photography and illuminated by infrared light, was quantified across midday, dusk, and night periods to explore possible effects of reef type (artificial vs. natural) on these patterns. Diurnal communities on natural reefs exhibited greater fish abundance, species richness, and functional diversity compared to artificial reefs. Furthermore, both types of reef communities exhibited a significant shift across the diel period, characterized by a decline in total fish density at night, especially for grunts (Haemulidae). Cross-habitat foraging migrations by diurnal or nocturnal species, such as haemulids, are likely central drivers of this twilight turnover and can represent important energy and nutrient subsidies. Time-lapse surveys provided more consistent measures of reef fish assemblages for the smaller artificial reef habitats, yet underestimated abundance of certain taxa and species richness on larger patch habitats when compared to the roving diver surveys. Time-lapse photography complemented with infrared light represent a valuable non-invasive approach to studying behavior of focal species and their fine-scale temporal dynamics in shallow-reef communities.

Does landscape context affect habitat value? The importance of seascape ecology in back-reef systems

Seascape ecology provides a useful framework from which to understand the processes governing spatial variability in ecological patterns. Seascape context, or the composition and pattern of habitat surrounding a focal patch, has the potential to impact resource availability, predator-prey interactions, and connectivity with other habitats. For my dissertation research, I combined a variety of approaches to examine how habitat quality for fishes is influenced by a diverse range of seascape factors in sub-tropical, back-reef ecosystems. In the first part of my dissertation, I examined how seascape context can affect reef fish communities on an experimental array of artificial reefs created in various seascape contexts in Abaco, Bahamas. I found that the amount of seagrass at large spatial scales was an important predictor of community assembly on these reefs. Additionally, seascape context had differing effects on various aspects of habitat quality for the most common reef species, White grunt Haemulon plumierii. The amount of seagrass at large spatial scales had positive effects on fish abundance and secondary production, but not on metrics of condition and growth. The second part of my dissertation focused on how foraging conditions for fish varied across a linear seascape gradient in the Loxahatchee River estuary in Florida, USA. Gray snapper, Lutjanus griseus, traded food quality for quantity along this estuarine gradient, maintaining similar growth rates and condition among sites. Additional work focused on identifying major energy flow pathways to two consumers in oyster-reef food webs in the Loxahatchee. Algal and microphytobenthos resource pools supported most of the production to these consumers, and body size for one of the consumers mediated food web linkages with surrounding mangrove habitats. All of these studies examined a different facet of the importance of seascape context in governing ecological processes occurring in focal habitats and underscore the role of connectivity among habitats in back-reef systems. The results suggest that management approaches consider the surrounding seascape when prioritizing areas for conservation or attempting to understand the impacts of seascape change on focal habitat patches. For this reason, spatially-based management approaches are recommended to most effectively manage back-reef systems.