Macroalgae Decrease Growth and Alter Microbial Community Structure of the Reef-Building Coral, Porites astreoides

With the continued and unprecedented decline of coral reefs worldwide, evaluating the factors that contribute to coral demise is of critical importance. As coral cover declines, macroalgae are becoming more common on tropical reefs. Interactions between these macroalgae and corals may alter the coral microbiome, which is thought to play an important role in colony health and survival. Together, such changes in benthic macroalgae and in the coral microbiome may result in a feedback mechanism that contributes to additional coral cover loss. To determine if macroalgae alter the coral microbiome, we conducted a field-based experiment in which the coral Porites astreoides was placed in competition with five species of macroalgae. Macroalgal contact increased variance in the coral-associated microbial community, and two algal species significantly altered microbial community composition. All macroalgae caused the disappearance of a γ-proteobacterium previously hypothesized to be an important mutualist of P. astreoides. Macroalgal contact also triggered: 1) increases or 2) decreases in microbial taxa already present in corals, 3) establishment of new taxa to the coral microbiome, and 4) vectoring and growth of microbial taxa from the macroalgae to the coral. Furthermore, macroalgal competition decreased coral growth rates by an average of 36.8%. Overall, this study found that competition between corals and certain species of macroalgae leads to an altered coral microbiome, providing a potential mechanism by which macroalgae-coral interactions reduce coral health and lead to coral loss on impacted reefs.

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. ^

Spatial variability in Florida Bay particulate organic matter composition: combining flow cytometry with stable isotope analyses

Long-term management plans for restoration of natural flow conditions through the Everglades increase the importance of understanding potential nutrient impacts of increased freshwater delivery on Florida Bay biogeochemistry. Planktonic communities respond quickly to changes in water quality, thus spatial variability in community composition and relationships to nutrient parameters must be understood in order to evaluate future downstream impacts of modifications to Everglades hydrology. Here we present initial results combining flow cytometry analyses of phytoplankton and bacterial populations (0.1–50 μm size fraction) with measurements of δ13C and δ15N composition and dissolved inorganic nutrient concentrations to explore proxies for planktonic species assemblage compositions and nutrient cycling. Particulate organic material in the 0.1–50 μm size fraction was collected from five stations in Northeastern and Western Florida Bay to characterize spatial variability in species assemblage and stable isotopic composition. A dense bloom of the picocyanobacterium, Synechococcus elongatus, was observed at Western Florida Bay sites. Smaller Synechococcus sp. were present at Northeast sites in much lower abundance. Bacteria and detrital particles were also more abundant at Western Florida Bay stations than in the northeast region. The highest abundance of detritus occurred at Trout Creek, which receives freshwater discharge from the Everglades through Taylor Slough. In terms of nutrient availability and stable isotopic values, the S. elongatus population in the Western bay corresponded to low DIN (0.5 μM NH 4 + ; 0.2 μM NO 3 − ) concentrations and depleted δ15N signatures ranging from +0.3 to +0.8‰, suggesting that the bloom supported high productivity levels through N2-fixation. δ15N values from the Northeast bay were more enriched (+2.0 to +3.0‰), characteristic of N-recycling. δ13C values were similar for all marine Florida Bay stations, ranging from −17.6 to −14.4‰, however were more depleted at the mangrove ecotone station (−25.5 to −22.3‰). The difference in the isotopic values reflects differences in carbon sources. These findings imply that variations in resource availability and nutrient sources exert significant control over planktonic community composition, which is reflected by stable isotopic signatures.

Seasonal fish community variation in headwater mangrove creeks in the southwestern Everglades: an examination of their role as dry-down refuges

The connectivity between the fish community of estuarine mangroves and that of freshwater habitats upstream remains poorly understood. In the Florida Everglades, mangrove-lined creeks link freshwater marshes to estuarine habitats downstream and may act as dry-season refuges for freshwater fishes. We examined seasonal dynamics in the fish community of ecotonal creeks in the southwestern region of Everglades National Park, specifically Rookery Branch and the North and watson rivers. Twelve low-order creeks were sampled via electrofishing, gill nets, and minnow traps during the wet season, transition period, and dry season in 2004-2005. Catches were greater in Rookery Branch than in the North and watson rivers, particularly during the transition period. Community composition varied seasonally in Rookery Branch, and to a greater extent for the larger species, reflecting a pulse of freshwater taxa into creeks as marshes upstream dried periodically. The pulse was short-lived, a later sample showed substantial decreases in freshwater fish numbers. No evidence of a similar influx was seen in the North and watson rivers, which drain shorter hydroperiod marshes and exhibit higher salinities. These results suggest that head-water creeks can serve as important dry-season refugia. Increased freshwater flow resulting from Everglades restoration may enhance this connectivity.

Patterns of Soil Bacteria and Canopy Community Structure Related to Tropical Peatland Development

Natural environmental gradients provide important information about the ecological constraints on plant and microbial community structure. In a tropical peatland of Panama, we investigated community structure (forest canopy and soil bacteria) and microbial community function (soil enzyme activities and respiration) along an ecosystem development gradient that coincided with a natural P gradient. Highly structured plant and bacterial communities that correlated with gradients in phosphorus status and soil organic matter content characterized the peatland. A secondary gradient in soil porewater NH4 described significant variance in soil microbial respiration and β-1-4-glucosidase activity. Covariation of canopy and soil bacteria taxa contributed to a better understanding of ecological classifications for biotic communities with applicability for tropical peatland ecosystems of Central America. Moreover, plants and soils, linked primarily through increasing P deficiency, influenced strong patterning of plant and bacterial community structure related to the development of this tropical peatland ecosystem.

A Comparative Study of Concurrent Acoustic and Diver Survey Data, and Fish Community Descriptions of a High Latitude Coral Reef, Florida, USA

Fisheries independent data on relatively unstudied nekton communities were used to explore the efficacy of new tools to be applied in the investigation of shallow coastal coral reef habitats. These data obtained through concurrent diver visual and acoustic surveys provided descriptions of spatial community distribution patterns across seasonal temporal scales in a previously undocumented region. Fish density estimates by both diver and acoustic methodologies showed a general agreement in ability to detect distributional patterns across reef tracts, though magnitude of density estimates were different. Fish communities in southeastern Florida showed significant trends in spatial distribution and seasonal abundance, with higher estimates of biomass obtained in the dry season. Further, community composition shifted across reef tracts and seasons as a function of the movements of several key reef species.

The L-31E Surface Water Rediversion Project Final Report: Implementation, Results, and Recommendations

Throughout the Biscayne Bay watershed, existing coastal wetland communities have been cut off from sheet flow for decades. With the expectation that reconnection of these wetlands to upstream water sources would alter existing hydrologic conditions and recreate a more natural sheet flow to Biscayne National Park, a demonstration project on freshwater rediversion was undertaken. The objectives of the project were to document the effects of freshwater diversion on: (a) swamp and nearshore water chemistry and hydrology; (b) soil development processes; (c) macrophyte and benthic algal community composition, structure and production; (d) abundance of epiphytic and epibenthic invertebrates; (e) zonation, production, and phenology of primary producers in the nearshore environment, and (f) exchanges of nutrients and particulates between nearshore and mangrove ecosystems.

Black band disease of corals: Ecology and physiology of Phormidium corallyticum

Black band disease of corals consists of a microbial community dominated by the cyanobacteriurn Phormidium corallyticum. The disease primarily affects reef-framework coral species, Active black band disease continually opens up new substrate in reef environments by destroying coral tissue as the disease line advances across the surface of infected colonies. A field study was carried out to determine the abundance and distribution of black band disease on the reef building corals in the Florida Keys. During July of 1992 and 1993, up to 0.72% of coral colonies were infected with black band disease. Analysis of the distribution showed that the disease was clumped. Seasonal patters varied, with some coral colonies infected year round, others exhibiting reinfection from summer 1992 to summer 1993, and some colonies infected for one year only. Statistical analysis of black band disease incidence in relation to various environmental parameters revealed that black band disease was associated with relatively shallow water depths, higher temperatures, elevated nitrite levels, and decreased ortho-phosphate levels. Additional field studies determined recovery of scleractinian coral colonies damaged or killed through the activities of black band disease over a five-year period. These studies determined if the newly exposed substrate was recolonized through scleractinian recruitment, if there was overgrowth of the damaged areas by the formerly diseased colony, or if coral tissue destruction continued after the cessation of black band disease activity. Tissue loss continued on all coral colonies with only one colony exhibiting new tissue growth. The majority of recolonization was by non-reef-framework corals and octocorallians, limited recruitment by framework species was observed. Physiological studies of P. corallyticum were carried out to investigate the photosynthetic capacity of this cyanobacterium, and to determine if this species has the ability to fix dinitrogen. The results of this research demonstrated that P. corallyticum reaches maximum photosynthetic rates at very low light intensities (27.9 μE/m/sec), and that P. corallyticum is able to carry out oxygenic photosynthesis in the presence of sulfide, an ability that is uncommon in prokaryotic organisms. ^

Diversity of Hymenoptera, cultivated plants and management practices in home garden agroecosystems, Kyrgyz Republic

Pollination-dependent fruit trees grown in home gardens play an important role in the agricultural based economy of Central Asian countries, yet little is known about the status of pollinator communities, the cultivated plant composition or the factors that influence management practices in Kyrgyz home garden agroecosystems. As agricultural systems are human created and managed, a logical approach to their study blends anthropological and ecological methods, an ethnoecological approach. Over three years, I investigated how species richness and abundance of Hymenoptera, cultivated plants, and home garden management were related using quantitative and qualitative methods in the Issyk-kul Man and Biosphere reserve. Structured surveys were undertaken with heads of households using a random sample stratified by village. Gardens were then mapped with participation of household members to inventory edible species in gardens, most of which are pollinator-dependent, and to compare home garden diversity as reported by respondents during interviews. Apple diversity was studied to the variety level to understand respondents’ classification system in the context of in situ agrobiodiversity conservation. Household members identified 52 edible plant species when mapping the garden, compared with 32 reported when interviewed. The proportion of plant species received from others through exchange and the number of plots cultivated significantly explained the variation in edible plant diversity among gardens. Insects were sampled in gardens and orchards to determine potential pollinator community composition and the effect of different management practices on Hymenoptera richness and abundance. I collected 756 Hymenoptera individuals (56 bee; 12 wasp species); 12 species were new records for Kyrgyzstan or within Kyrgyzstan. Economic pressures to intensify cultivation could impact management practices that currently promote diversity. A home garden development initiative was undertaken to study management practice improvement. Participants in the initiative had higher adoption rates than controls of management practices that improve long-term yield, ecological sustainability and stability of home gardens. Home gardens, as currently managed, support abundant and diverse pollinator communities and have high cultivated plant diversity with few differences in community composition between garden management types.

A multi-faceted diagnostic approach to lung infections in patients with cystic fibrosis

One in 3,000 people in the US are born with cystic fibrosis (CF), a genetic disorder affecting the reproductive system, pancreas, and lungs. Lung disease caused by chronic bacterial and fungal infections is the leading cause of morbidity and mortality in CF. Identities of the microbes are traditionally determined by culturing followed by phenotypic and biochemical assays. It was first thought that the bacterial infections were caused by a select handful of bacteria such as S. aureus, H. influenzae, B. cenocepacia, and P. aeruginosa. With the advent of PCR and molecular techniques, the polymicrobial nature of the CF lung became evident. The CF lung contains numerous bacteria and the communities are diverse and unique to each patient. The total complexity of the bacterial infections is still being determined. In addition, only a few members of the fungal communities have been identified. Much of the fungal community composition is still a mystery. This dissertation addresses this gap in knowledge. A snap shot of CF sputa bacterial community was obtained using the length heterogeneity-PCR community profiling technique. The profiles show that south Florida CF patients have a unique, diverse, and dynamic bacterial community which changes over time. The identities of the bacteria and fungi present were determined using the state-of-the-art 454 sequencing. Sequencing results show that the CF lung microbiome contains commonly cultured pathogenic bacteria, organisms considered a part of the healthy core biome, and novel organisms. Understanding the dynamic changes of these identified microbes will ultimately lead to better therapeutical interventions. Early detection is key in reducing the lung damage caused by chronic infections. Thus, there is a need for accurate and sensitive diagnostic tests. This issue was addressed by designing a bacterial diagnostic tool targeted towards CF pathogens using SPR. By identifying the organisms associated with the CF lung and understanding their community interactions, patients can receive better treatment and live longer.

Treefrogs in Forested Swamps at the La Selva Biological Station: Assemblage Variation through Space and Time

Swamp-breeding treefrogs form conspicuous components of many tropical forest sites, yet remain largely understudied. The La Selva Biological Station, a rainforest reserve in Costa Rica, harbors a rich swamp-breeding treefrog fauna that has been studied in only one of the many swamps found at the site. To understand if the species composition of treefrogs at La Selva varies over space or time, frogs were censused in 1982-83, 1994-95, 2005 and 2011 at two ponds located in the reserve. Data on treefrog habitat utilization were also collected. Species composition varied spatially only in 2011. Temporal variation was observed at both ponds for all groups tested. Habitat use varied among species and between swamps. The pattern of variation suggests that temporally dynamic systems such as temporary Neotropical forest swamps will converge and diverge in species composition over time.

Variable responses within epiphytic and benthic microalgal communities to nutrient enrichment

We examined the spatial extent of nitrogen (N) and phosphorus (P) limitation of each of the major benthic primary producer groups in Florida Bay (seagrass, epiphytes, macroalgae, and benthic microalgae) and characterized the shifts in primary producer community composition following nutrient enrichment. We established 24 permanent 0.25-m2 study plots at each of six sites across Florida Bay and added N and P to the sediments in a factorial design for 18 mo. Tissue nutrient content of the turtlegrass Thalassia testudinum revealed a spatial pattern in P limitation, from severe limitation in the eastern bay (N:P > 96:1), moderate limitation in two intermediate sites (approximately 63:1), and balanced with N availability in the western bay (approximately 31:1). P addition increased T. testudinum cover by 50-75% and short-shoot productivity by up to 100%, but only at the severely P-limited sites. At sites with an ambient N:P ratio suggesting moderate P limitation, few seagrass responses to nutrients occurred. Where ambient T. testudinum tissue N:P ratios indicated N and P availability was balanced, seagrass was not affected by nutrient addition but was strongly influenced by disturbance (currents, erosion). Macroalgal and epiphytic and benthic microalgal biomass were variable between sites and treatments. In general, there was no algal overgrowth of the seagrass in enriched conditions, possibly due to the strength of seasonal influences on algal biomass or regulation by grazers. N addition had little effect on any benthic primary producers throughout the bay. The Florida Bay benthic primary producer community was P limited, but P-induced alterations of community structure were not uniform among primary producers or across Florida Bay and did not always agree with expected patterns of nutrient limitation based on stoichiometric predictions from field assays of T. testudinum tissue N:P ratios.

Periphyton as an indicator of restoration in the Everglades

Periphyton communities dominate primary production in much of the Florida Everglades wetland and therefore contribute to soil production, ecosystem metabolism and secondary production as well as the composition of dependent communities. Decades of research in the Everglades have supported research findings from other wetland types that cumulatively show that periphyton communities respond very rapidly to alterations in the two dominant drivers of wetland structure and function—hydrology and water quality. Hydrology controls periphyton productivity and composition by regulating moisture availability, substrate types available for colonization and supply of nutrients. Nutrients, particularly the limiting nutrient in this system, phosphorus (P), control levels of production and community composition. Because periphyton communities are well-established to be related to hydrology and water quality, an indicator was developed based on three periphyton attributes: abundance, quality (i.e., nutrient content) and community composition. This assessment tool offers a qualitative assessment of ecosystem response to potential changes in management activities at a time scale appropriate for active management. An example is provided of how the indicator can be used to assess the current water quality and hydrological conditions from high-density spatial surveys. Detected patterns of deterioration align with expectations derived from model predictions and known sources of nutrients and unnatural hydrologic regimes. If employed adaptively in ecosystem management, this tool can be used to both detect and react to change before the system has been irreparably altered.

Decadal Change in Vegetation and Soil Phosphorus Pattern across the Everglades Landscape

Wetlands respond to nutrient enrichment with characteristic increases in soil nutrients and shifts in plant community composition. These responses to eutrophication tend to be more rapid and longer lasting in oligotrophic systems. In this study, we documented changes associated with water quality from 1989 to 1999 in oligotrophic Everglades wetlands. We accomplished this by resampling soils and macrophytes along four transects in 1999 that were originally sampled in 1989. In addition to documenting soil phosphorus (P) levels and decadal changes in plant species composition at the same sites, we report macrophyte tissue nutrient and biomass data from 1999 for future temporal comparisons. Water quality improved throughout much of the Everglades in the 1990s. In spite of this improvement, though, we found that water quality impacts worsened during this time in areas of the northern Everglades (western Loxahatchee National Wildlife Refuge [NWR] and Water Conservation Area [WCA] 2A). Zones of high soil P (exceeding 700 mg P kg−1 dry wt. soil) increased to more than 1 km from the western margin canal into the Loxahatchee NWR and more than 4 km from northern boundary canal into WCA-2A. This doubling of the high soil P zones since 1989 was paralleled with an expansion of cattail (Typha spp.)-dominated marsh in both regions. Macrophyte species richness declined in both areas from 1989 to 1999 (27% in the Loxahatchee NWR and 33% in WCA-2A). In contrast, areas well south of the Everglades Agricultural Area, including WCA-3A and Everglades National Park (ENP), did not decline during this time. We found no significant decadal change in plant community patterns from 1989 and 1999 along transects in southern WCA-3A or Shark River Slough (ENP). Our 1999 sampling also included a new transect in Taylor Slough (ENP), which will allow change analysis here in the future. Regular sampling of these transects, to verify decadal-scale environmental impacts or improvements, will continue to be an important tool for long-term management and restoration of the Everglades.

Responses of sawgrass and spikerush to variation in hydrologic drivers and salinity in Southern Everglades marshes

Aboveground net primary production (ANPP) by the dominant macrophyte and plant community composition are related to the changing hydrologic environment and to salinity in the southern Everglades, FL, USA. We present a new non-destructive ANPP technique that is applicable to any continuously growing herbaceous system. Data from 16 sites, collected from 1998 to 2004, were used to investigate how hydrology and salinity controlled sawgrass (Cladium jamaicense Crantz.) ANPP. Sawgrass live biomass showed little seasonal variation and annual means ranged from 89 to 639 gdw m)2. Mortality rates were 20–35% of live biomass per 2 month sampling interval, for biomass turnover rates of 1.3–2.5 per year. Production by C. jamaicense was manifest primarily as biomass turnover, not as biomass accumulation. Rates typically ranged from 300 to 750 gdw m)2 year)1, but exceeded 1000 gdw m)2 year)1 at one site and were as high as 750 gdw m)2 year)1 at estuarine ecotone sites. Production was negatively related to mean annual water depth, hydroperiod, and to a variable combining the two (depth-days). As water depths and hydroperiods increased in our southern Everglades study area, sawgrass ANPP declined. Because a primary restoration goal is to increase water depths and hydroperiods for some regions of the Everglades, we investigated how the plant community responded to this decline in sawgrass ANPP. Spikerush (Eleocharis sp.) was the next most prominent component of this community at our sites, and 39% of the variability in sawgrass ANPP was explained by a negative relationship with mean annual water depth, hydroperiod, and Eleocharis sp. density the following year. Sawgrass ANPP at estuarine ecotone sites responded negatively to salinity, and rates of production were slow to recover after high salinity years. Our results suggest that ecologists, managers, and the public should not necessarily interpret a decline in sawgrass that may result from hydrologic restoration as a negative phenomenon.