Investigation of an acetate-fed denitrifying microbial community by stable isotope probing, full-cycle rRNA analysis, and fluorescent in situ hybridization-microautoradiography

The acetate-utilizing microbial consortium in a full-scale activated sludge process was investigated without prior enrichment using stable isotope probing (SIP). [C-13]acetate was used in SIP to label the DNA of the denitrifiers. The [C-13]DNA fraction that was extracted was subjected to a full-cycle rRNA analysis. The dominant 16S rRNA gene phylotypes in the C-13 library were closely related to the bacterial families Comamonadaceae and Rhodocyclaceae in the class Betaproteobacteria. Seven oligonucleotide probes for use in fluorescent in situ hybridization (FISH) were designed to specifically target these clones. Application of these probes to the sludge of a continuously fed denitrifying sequencing batch reactor (CFDSBR) operated for 16 days revealed that there was a significant positive correlation between the CFDSBR denitrification rate and the relative abundance of all probe-targeted bacteria in the CFDSBR community. FISH-microautoradiography demonstrated that the DEN581 and DEN124 probe-targeted cells that dominated the CFDSBR were capable of taking Up [C-14] acetate under anoxic conditions. Initially, DEN444 and DEN1454 probe-targeted bacteria also dominated the CFDSBR biomass, but eventually DEN581 and DEN124 probe-targeted bacteria were the dominant bacterial groups. All probe-targeted bacteria assessed in this study were denitrifiers capable of utilizing acetate as a source of carbon. The rapid increase in the number of organisms positively correlated with the immediate increase in denitrification rates observed by plant operators when acetate is used as an external source of carbon to enhance denitrification. We suggest that the impact of bacteria on activated sludge subjected to intermittent acetate supplementation should be assessed prior to the widespread use of acetate in the waste-water industry to enhance denitrification.

Structure of a cellulose degrading bacterial community during anaerobic digestion

It is widely accepted that cellulose is the rate-limiting substrate in the anaerobic digestion of organic solid wastes and that cellulose solubilisation is largely mediated by surface attached bacteria. However, little is known about the identity or the ecophysiology of cellulolytic microorganisms from landfills and anaerobic digesters. The aim of this study was to investigate an enriched cellulolytic microbial community from an anaerobic batch reactor. Chemical oxygen demand balancing was used to calculate the cellulose solubilisation rate and the degree of cellulose solubilisation. Fluorescence in situ hybridisation (FISH) was used to assess the relative abundance and physical location of three groups of bacteria belonging to the Clostridium lineage of the Firmicutes that have been implicated as the dominant cellulose degraders in this system. Quantitation of the relative abundance using FISH showed that there were changes in the microbial community structure throughout the digestion. However, comparison of these results to the process data reveals that these changes had no impact on the cellulose solubilisation in the reactor. The rate of cellulose solubilisation was approximately stable for much of the digestion despite changes in the cellulolytic population. The solubilisation rate appears to be most strongly affected by the rate of surface area colonisation and the biofilm architecture with the accepted model of first order kinetics due to surface area limitation applying only when the cellulose particles are fully covered with a thin layer of cells. (c) 2005 Wiley Periodicals, Inc.

Endoparasite communities of five fish species (Labridae : Cheilininae) from Lizard Island: how important is the ecology and phylogeny of the hosts?

The parasite community of animals is generally influenced by host physiology, ecology, and phylogeny. Therefore, sympatric and phylogenetically related hosts with similar ecologies should have similar parasite communities. To test this hypothesis we surveyed the endoparasites of 5 closely related cheilinine fishes (Labridae) from the Great Barrier Reef. They were Cheilinus chlorounts, C. trilobatus, C. fasciatils, Epibulus insidiator and OxYcheilinus diagrainnia. VVe examined the relationship between parasitological variables (richness, abundance and diversity) and host characteristics (bodv weight, diet and phuylogeny). The 5 fishes had 31 parasite species with 9-18 parasite species per fish species. Cestode larvae (mostly Tetraphyllidea) were the most abundant and prevalent parasites followed by nematodes and digeneans. Parasites, body size and diet of hosts differed between fish species. In general, body weight, diet and host phylogeny each explained some of the variation in richness and composition of parasites among the fishes. The 2 most closely related species, Cheilinus chlorourus and C. trilobatus, had broadly similar parasites but the Other fish species differed significantly in all variables. However, there was no all -encompassing pattern. This may, be because different lineages of parasites may react differently to ecological variables. We also argue that adult parasites may respond principally to host diet. In contrast, larval parasite composition may respond both to host diet and predator-prey interactions because this is the path by which many, parasites complete their life-cycles. Finally, variation in parasite phylogeny and parasite life-cycles among hosts likely increase the complexity of the system making it difficult to find all-encompassing patterns between host characteristics and parasites, particularly when all the species in rich parasite communities are considered.

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. ^

Spatial scale and abundance patterns of large fish communities in freshwater marshes of the Florida Everglades

Anthropogenic habitat alterations and water-management practices have imposed an artificial spatial scale onto the once contiguous freshwater marshes of the Florida Everglades. To gain insight into how these changes may affect biotic communities, we examined whether variation in the abundance and community structure of large fishes (SL . 8 cm) in Everglades marshes varied more at regional or intraregional scales, and whether this variation was related to hydroperiod, water depth, floating mat volume, and vegetation density. From October 1997 to October 2002, we used an airboat electrofisher to sample large fishes at sites within three regions of the Everglades. Each of these regions is subject to unique watermanagement schedules. Dry-down events (water depth , 10 cm) occurred at several sites during spring in 1999, 2000, 2001, and 2002. The 2001 dry-down event was the most severe and widespread. Abundance of several fishes decreased significantly through time, and the number of days post-dry-down covaried significantly with abundance for several species. Processes operating at the regional scale appear to play important roles in regulating large fishes. The most pronounced patterns in abundance and community structure occurred at the regional scale, and the effect size for region was greater than the effect size for sites nested within region for abundance of all species combined, all predators combined, and each of the seven most abundant species. Non-metric multi-dimensional scaling revealed distinct groupings of sites corresponding to the three regions. We also found significant variation in community structure through time that correlated with the number of days post-dry-down. Our results suggest that hydroperiod and water management at the regional scale influence large fish communities of Everglades marshes.

The influence of body size on the ecology of coastal fish predators in the Bahamas

Body size is a fundamental structural characteristic of organisms, determining critical life history and physiological traits, and influencing population dynamics, community structure, and ecosystem function. For my dissertation, I focused on effects of body size on habitat use and diet of important coastal fish predators, as well as their influence on faunal communities in Bahamian wetlands. First, using acoustic telemetry and stable isotope analysis, I identified high variability in movement patterns and habitat use among individuals within a gray snapper (Lutjanus griseus) and schoolmaster snapper (L. apodus) population. This intrapopulation variation was not explained by body size, but by individual behavior in habitat use. Isotope values differed between individuals that moved further distances and individuals that stayed close to their home sites, suggesting movement differences were related to specific patterns of foraging behavior. Subsequently, while investigating diet of schoolmaster snapper over a two-year period using stomach content and stable isotope analyses, I also found intrapopulation diet variation, mostly explained by differences in size class, individual behavior and temporal variability. I then developed a hypothesis-testing framework examining intrapopulation niche variation between size classes using stable isotopes. This framework can serve as baseline to categorize taxonomic or functional groupings into specific niche shift scenarios, as well as to help elucidate underlying mechanisms causing niche shifts in certain size classes. Finally, I examined the effect of different-sized fish predators on epifaunal community structure in shallow seagrass beds using exclusion experiments at two spatial scales. Overall, I found that predator effects were rather weak, with predator size and spatial scale having no impact on the community. Yet, I also found some evidence of strong interactions on particular common snapper prey. As Bahamian wetlands are increasingly threatened by human activities (e.g., overexploitation, habitat degradation), an enhanced knowledge of the ecology of organisms inhabiting these systems is crucial for developing appropriate conservation and management strategies. My dissertation research contributed to this effort by providing critical information about the resource use of important Bahamian fish predators, as well as their effect on faunal seagrass communities.

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.

Life history trade-offs and community dynamics of small fishes in a seasonally pulsed wetland

We used a one-dimensional, spatially explicit model to simulate the community of small fishes in the freshwater wetlands of southern Florida, USA. The seasonality of rainfall in these wetlands causes annual fluctuations in the amount of flooded area. We modeled fish populations that differed from each other only in efficiency of resource utilization and dispersal ability. The simulations showed that these trade-offs, along with the spatial and temporal variability of the environment, allow coexistence of several species competing exploitatively for a common resource type. This mechanism, while sharing some characteristics with other mechanisms proposed for coexistence of competing species, is novel in detail. Simulated fish densities resembled patterns observed in Everglades empirical data. Cells with hydroperiods less than 6 months accumulated negligible fish biomass. One unique model result was that, when multiple species coexisted, it was possible for one of the coexisting species to have both lower local resource utilization efficiency and lower dispersal ability than one of the other species. This counterintuitive result is a consequence of stronger effects of other competitors on the superior species.

Assessing the net effect of anthropogenic disturbance on aquatic communities in wetlands: community structure relative to distance from canals

Anthropogenic alterations of natural hydrology are common in wetlands and often increase water permanence, converting ephemeral habitats into permanent ones. Since aquatic organisms segregate strongly along hydroperiod gradients, added water permanence caused by canals can dramatically change the structure of aquatic communities. We examined the impact of canals on the abundance and structure of wetland communities in South Florida, USA. We sampled fishes and macroinvertebrates from marsh transects originating at canals in the central and southern Everglades. Density of all aquatic organisms sampled increased in the immediate proximity of canals, but was accompanied by few compositional changes based on analysis of relative abundance. Large fish (>8 cm), small fish (<8 >cm) and macroinvertebrates (>5 mm) increased in density within 5 m of canals. This pattern was most pronounced in the dry season, suggesting that canals may serve as dry-down refugia. Increases in aquatic animal density closely matched gradients of phosphorus enrichment that decreased with distance from canals. Thus, the most apparent impact of canals on adjacent marsh communities was as conduits for nutrients that stimulated local productivity; any impact of their role as sources of increased sources of predators was not apparent. The effect of predation close to canals was overcompensated by increased secondary productivity and/or immigration toward areas adjacent to canals in the dry season. Alternatively, the consumptive effect of predatory fishes using canals as dry-season refuges is very small or spread over the expanse of marshes with open access to canals.

Disturbance frequency and community structure in a twenty-five year intervention study

Models of community regulation commonly incorporate gradients of disturbance inversely related to the role of biotic interactions in regulating intermediate trophic levels. Higher trophic-level organisms are predicted to be more strongly limited by intermediate levels of disturbance than are the organisms they consume. We used a manipulation of the frequency of hydrological disturbance in an intervention analysis to examine its effects on small-fish communities in the Everglades, USA. From 1978 to 2002, we monitored fishes at one long-hydroperiod (average 350 days) and at one short-hydroperiod (average 259 days; monitoring started here in 1985) site. At a third site, managers intervened in 1985 to diminish the frequency and duration of marsh drying. By the late 1990s, the successional dynamics of density and relative abundance at the intervention site converged on those of the long-hydroperiod site. Community change was manifested over 3 to 5 years following a dry-down if a site remained inundated; the number of days since the most recent drying event and length of the preceding dry period were useful for predicting population dynamics. Community dissimilarity was positively correlated with the time since last dry. Community dynamics resulted from change in the relative abundance of three groups of species linked by life-history responses to drought. Drought frequency and intensity covaried in response to hydrological manipulation at the landscape scale; community-level successional dynamics converged on a relatively small range of species compositions when drought return-time extended beyond 4 years. The density of small fishes increased with diminution of drought frequency, consistent with disturbance-limited community structure; less-frequent drying than experienced in this study (i.e., longer return times) yields predator-dominated regulation of small-fish communities in some parts of the Everglades.

Indirect and direct controls of macroinvertebrates and small fish by abiotic factors and trophic interactions in the Florida Everglades

1. The roles of nutrients, disturbance and predation in regulating consumer densities have long been of interest, but their indirect effects have rarely been quantified in wetland ecosystems. The Florida Everglades contains gradients of hydrological disturbance (marsh drying) and nutrient enrichment (phosphorus), often correlated with densities of macroinvertebrate infauna (macroinvertebrates inhabiting periphyton), small fish and larger invertebrates, such as snails, grass shrimp, insects and crayfish. However, most causal relationships have yet to be quantified. 2.  We sampled periphyton (content and community structure) and consumer (small omnivores, carnivores and herbivores, and infaunal macroinvertebrates inhabiting periphyton) density at 28 sites spanning a range of hydrological and nutrient conditions and compared our data to seven a priori structural equation models. 3.  The best model included bottom-up and top-down effects among trophic groups and supported top-down control of infauna by omnivores and predators that cascaded to periphyton biomass. The next best model included bottom-up paths only and allowed direct effects of periphyton on omnivore density. Both models suggested a positive relationship between small herbivores and small omnivores, indicating that predation was unable to limit herbivore numbers. Total effects of time following flooding were negative for all three consumer groups even when both preferred models suggested positive direct effects for some groups. Total effects of nutrient levels (phosphorus) were positive for consumers and generally larger than those of hydrological disturbance and were mediated by changes in periphyton content. 4.  Our findings provide quantitative support for indirect effects of nutrient enrichment on consumers, and the importance of both algal community structure and periphyton biomass to Everglades food webs. Evidence for top-down control of infauna by omnivores was noted, though without substantially greater support than a competing bottom-up-only model.

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.

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.

Density-Dependent Effects of Coral Reef Restoration on Herbivory and Community Interactions

Coral reefs are among the most productive ecosystems in the world. Yet, with their recent declines due to disease, climate change, and overfishing, restoration of these habitats is one of the main concerns for ecologists, resource managers, and government organizations. Coral reef restoration aims to promote key ecosystem processes to shift these habitats to their historical state of high coral cover, but few studies have focused on effective ways to promote resilience. In addition, little is known about the impact of restoration on the fish communities. The aim of this study is to understand how the community of herbivorous fishes is affected by the density of coral outplants inside a special protection area located in the Florida Keys National Marine Sanctuary. Grazing rates, number of visits and time spent foraging were compared using video footage of sites previously devoid of corals, and six months after coral restorations had occurred. Coral transplantations did not appear to attract herbivores nor increase grazing rates of fishes. Instead Sparisoma and Acanthurus fishes appear to respond to changes in the environment by modifying their grazing behavior. However, there was an observed increase in visits by Acanthurus species after transplantation for all the sites sampled within the reef. These fishes seemed to prefer low coral cover sites for grazing. This study highlights the importance of examining coral restorations impacts at the community level. Understanding how restoration influences herbivores and other guilds of reef fishes will allow individuals to not only determine if these habitats are returning to their “original” state, but provide more information on the ways these systems cope with changes in the environment.

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.