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. ^

Acoustic telemetry studies of bonefish (Albula vulpes ) movement around Andros Island, Bahamas: Implications for species management

Bonefish (Albula spp.) support an economically important catch-and-release recreational fishery, as well as artisanal harvesting, in The Bahamas. Little is known about the large-scale movement patterns of bonefish, yet such information is essential for proper species conservation and management. ^ I used acoustic telemetry to determine large-scale movement patterns of bonefish around Andros, Bahamas, in conjunction with presumed spawning migrations. I conclude that bonefish travel long distances from shallow flats to pre-spawning aggregation sites in proximity to off-shore reef locations. Off-shore movement to deeper reef locations occurs around both new and full moons. This study has also confirmed anecdotal reports that the North Bight is an important spawning migration corridor for bonefish. ^ This information is critical for the protection of bonefish and identifies important habitats (e.g. migration corridors and pre-spawning aggregations) on Andros that warrant protection from coastal degradation or fishing pressures. ^

Repetitive DNA fragments as taxonomic markers for {\it Penaeus\/} sibling taxa (Decapoda: Dendrobranchiata: Penaeidae) from the southern terminus of the Florida peninsula, U.S.A.

Sympatric populations of P. brasiliensis and P. duorarum from Biscayne Bay, Florida, revealed species-specific satellite DNA organizational patterns with the restriction endonuclease EcoRI. The species-specific satellite DNA patterns can be explained as resulting from differential amplification/deletion events having altered monomer arrays after the divergence of these two species. Two discontinuous populations of P. duorarum (Biscayne Bay and Dry Tortugas) were found to exhibit distinct EcoRI satellite fragment patterns; BamHI repetitive fragments specific to the Dry Tortugas P. duorarum population were also detected. In addition, the evolutionary conservation of the Penaeus (Farfantepenaeus) satellites was investigated. The putative conservation of sequences related to one cloned P. duorarum satellite monomer unit suggests that the FTR satellite DNA family may not only be of use as a genome tag to distinguish between sibling and cryptic Penaeus species but may also serve as a probe to better understand decapod crustacean genome organization and evolution. ^

Antibacterial proteins and peptides in nurse shark ( Ginglymostoma cirratum) peripheral blood leukocytes

In many vertebrate and invertebrate species mediators of innate immunity include antimicrobial peptides (AMPs) such as peptide fragments of histones and other proteins with previously ascribed different functions. Shark AMPs have not been described and this research examines the antibacterial activity of nurse shark (Ginglymostoma cirratum) peripheral blood leukocyte lysates. Screening of lysates prepared by homogenizing unstimulated peripheral blood leukocytes identified muramidase (lysozyme-like) and non-muramidase antibacterial activity. Lysates were tested for lysozyme using the lysoplate assays, and antibacterial (AB) activity was assayed for by a microdilution growth assay that was developed using Planococcus citreus as the target bacterium. Fractionation of crude lysates by ion exchange and affinity chromatography was followed by a combination of SDS-PAGE with LC/MS-MS and/or N-terminal sequence analysis of low molecular weight protein bands (<20 kDa). This yielded several peptides with amino acid sequence similarity to lysozyme, ubiquitin, hemoglobin, human histones H2A, H2B and H4 and to antibacterial histone fragments of the catfish and the Asian toad. Not all peptide sequences corresponded to peptides potentially antibacterial. The correlation of a specific protein band in active lysate fractions was accomplished by employing the acid-urea gel overlay assays in which AB activity was seen as zones of growth inhibition on a lawn of P. citreus at a position corresponding to that of the putative AB protein band. This study is the first to describe putative AMPs in the shark and their potential role in innate immunity.^

Vegetation dynamics and their implications for the management of wetlands in the lowlands of Nepal

The maintenance of species richness is often a priority in the management of nature reserves, where consumptive use of resources is generally prohibited. The purpose of this research was to improve management by understanding the vegetation dynamics in the lowlands of Nepal. The objectives were to determine vegetation associations in relation to environments and human-induced disturbances that affect vegetation dynamics on floodplains, where upstream barrages had altered flooding patterns, and consumptive use of plant resources was influencing natural processes. Floodplain vegetation in relation to physical environments and disturbances were studied along transects, perpendicular to the course of the Mahakali River in the western Terai, Nepal. Forest structural changes were studied for three years in ten plots. A randomized split-block experiment with nine burning and grazing treatments was performed in seasonally flooded grasslands. A semi-structured questionnaire was used to assess people's socio-economic status, natural resource use patterns and conservation attitudes. ^ Elevation, soil organic matter, nitrogen, percentage of sand and grazing intensity were significant in delineating herbaceous vegetation assemblages, whereas elevation and livestock grazing were significant in defining forest type boundaries. On the floodplain islands, highly grazed Dalbergia sissoo-Acacia catechu forests were devoid of understory woody vegetation, but the lightly grazed D. sissoo-mixed forests had a well-developed second canopy layer, comprising woody species other than D. sissoo and A. catechu. In grasslands, species richness and biomass production were highest at intermediate disturbance level represented by the lightly grazed and ungrazed early-burned treatments. Ethnicity, education and resource use patterns were important in influencing conservation attitudes. A succession towards the mixed forests would occur in D. sissoo-dominated floodplain forests, where dams and barrages reduce flooding and associated fluvial processes, and if livestock grazing is stopped, as occasionally suggested by nature conservationists. In seasonally flooded grasslands, early burning with moderate grazing would enhance the species diversity and productivity. There is a need to implement a participatory integrated wetland management plan, to include community development, education and off farm income generation, to assure participatory conservation and management of wetlands in Nepal. ^

The effects of climate on the growth and physiology of tropical rainforest trees

Tropical rainforests account for more than a third of global net primary production and contain more than half of the global forest carbon. Though these forests are a disproportionately important component of the global carbon cycle, the relationship between rainforest productivity and climate remains poorly understood. Understanding the link between current climate and rainforest tree stem diameter increment, a major constituent of forest productivity, will be crucial to efforts at modeling future climate and rainforest response to climate change. This work reports the physiological and stem growth responses to micrometeorological and phenological states of ten species of canopy trees in a Costa Rican wet tropical forest at sub-annual time intervals. I measured tree growth using band dendrometers and estimated leaf and reproductive phenological states monthly. Electronic data loggers recorded xylem sap flow (an indicator of photosynthetic rate) and weather at half-hour intervals. An analysis of xylem sap flow showed that physiological responses were independent of species, which allowed me to construct a general model of weather driven sap flow rates. This model predicted more than eighty percent of climate driven sap flow variation. Leaf phenology influenced growth in three of the ten species, with two of these species showing a link between leaf phenology and weather. A combination of rainfall, air temperature, and irradiance likely provided the cues that triggered leaf drop in Dipteryx panamensis and Lecythis ampla. Combining the results of the sap flow model, growth, and the climate measures showed tree growth was correlated to climate, though the majority of growth variation remained unexplained. Low variance in the environmental variables and growth rates likely contributed to the large amount of unexplained variation. A simple model that included previous growth increment and three meteorological variables explained from four to nearly fifty percent of the growth variation. Significant growth carryover existed in six of the ten species, and rainfall was positively correlated to growth in eight of the ten species. Minimum nighttime temperature was also correlated to higher growth rates in five of the species and irradiance in two species. These results indicate that tropical rainforest tree trunks could act as carbon sinks if future climate becomes wetter and slightly warmer. ^

Specificity, stability and comparative physiology of coral-Symbiodinium mutualisms: Evaluating the potential for acclimation and/or adaptation in reef corals

The relationship between reef corals and endosymbiotic dinoflagellates is fundamental to the existence of coral reefs. To evaluate the fidelity of coral-Symbiodinium mutualisms, corals maintained in aquaria for years were analyzed by denaturant gradient gel electrophoresis (DGGE). Comparing Symbiodinium populations of captive aquarium colonies with known associations in nature is a practical way of examining partner flexibility. The finding of "normal" symbiont populations in corals existing under highly variable conditions supports the premise that most coral colonies possess stable associations. High sensitivity real-time PCR (rtPCR) was used to evaluate background populations of the putatively stress-tolerant Symbiodinium D in reef corals of the Caribbean. Analyses of samples collected during periods of environmental stability indicate the ability of Symbiodinium D to associate with a wider diversity of host taxa than previously recognized. To gain a broader perspective with regard to the ecology of Symbiodinium D1a, rtPCR and DGGE were used to evaluate the symbiont populations of reef corals from Barbados before and after the 2005 mass coral bleaching. Background populations were observed in 56% of the host genera prior to observations of bleaching. These findings indicate that 'stress', not 'bleaching', caused the displacement of 'natural' symbiont population and the opportunistic proliferation of D1a in many host taxa. Of the 12 host taxa monitored before and after the bleaching event, there was a 40% increase in colonies hosting Symbiodinium D1a. Together, these studies elucidate the mechanism responsible for recent observations reporting the emergence of Symbiodinium D following thermal disturbances. These observations are now most easily explained as the disproportionate growth of existing in hospite symbiont populations, rather than novel symbiont acquisition subsequent to bleaching. To evaluate the comparative "fitness" of corals able to host multiple symbiont types, rates of calcification were measured in P. verrucosa hosting either Symbiodinium C1b-c or D1 at elevated temperature. Rates of calcification decreased significantly for both host-symbiont combinations, but differences attributable to symbiont composition were not detected. This research improves our knowledge of the symbiosis biology and ecology of reef corals and contributes information necessary to most accurately predict the response of these ecosystems to global climate changes.

The Role of Agriculture and Food Consumption in Tropical Conservation

A growing human population, shifting human dietary habits, and climate change are negatively affecting global ecosystems on a massive scale. Expanding agricultural areas to feed a growing population drives extensive habitat loss, and climate change compounds stresses on both food security and ecosystems. Understanding the negative effects of human diet and climate change on agricultural and natural ecosystems provides a context within which potential technological and behavioral solutions can be proposed to help maximize conservation. The purpose of this research was to (1) examine the potential effects of climate change on the suitability of areas for commercial banana plantations in Latin America in the 2050s and how shifts in growing areas could affect protected areas; (2) test the ability of small unmanned aerial vehicles (UAVs) to map productivity of banana plantations as a potential tool for increasing yields and decreasing future plantation expansions; (3) project the effects on biodiversity of increasing rates of animal product consumption in developing megadiverse countries; and (4) estimate the capacity of global pasture biomass production and Fischer-Tropsch hydrocarbon synthesis (IGCC-FT) processing to meet electricity, gasoline and diesel needs. The results indicate that (1) the overall extent of areas suitable for conventional banana cultivation is predicted to decrease by 19% by 2050 because of a hotter and drier climate, but all current banana exporting countries are predicted to maintain some suitable areas with no effects on protected areas; (2) Spatial patterns of NDVI and ENDVI were significantly positively correlated with several metrics of fruit yield and quality, indicating that UAV systems can be used in banana plantations to map spatial patterns of fruit yield; (3) Livestock production is the single largest driver of habitat loss, and both livestock and feedstock production are increasing in developing biodiverse tropical countries. Reducing global animal product consumption should therefore be at the forefront of strategies aimed at reducing biodiversity loss; (4) Removing livestock from global pasture lands and instead utilizing the biomass production could produce enough energy to meet 100% of the electricity, gasoline, and diesel needs of over 40 countries with extensive grassland ecosystems, primarily in tropical developing countries.

The role of agriculture and food consumption in tropical conservation

A growing human population, shifting human dietary habits, and climate change are negatively affecting global ecosystems on a massive scale. Expanding agricultural areas to feed a growing population drives extensive habitat loss, and climate change compounds stresses on both food security and ecosystems. Understanding the negative effects of human diet and climate change on agricultural and natural ecosystems provides a context within which potential technological and behavioral solutions can be proposed to help maximize conservation. The purpose of this research was to (1) examine the potential effects of climate change on the suitability of areas for commercial banana plantations in Latin America in the 2050s and how shifts in growing areas could affect protected areas; (2) test the ability of small unmanned aerial vehicles (UAVs) to map productivity of banana plantations as a potential tool for increasing yields and decreasing future plantation expansions; (3) project the effects on biodiversity of increasing rates of animal product consumption in developing megadiverse countries; and (4) estimate the capacity of global pasture biomass production and Fischer-Tropsch hydrocarbon synthesis (IGCC-FT) processing to meet electricity, gasoline and diesel needs. The results indicate that (1) the overall extent of areas suitable for conventional banana cultivation is predicted to decrease by 19% by 2050 because of a hotter and drier climate, but all current banana exporting countries are predicted to maintain some suitable areas with no effects on protected areas; (2) Spatial patterns of NDVI and ENDVI were significantly positively correlated with several metrics of fruit yield and quality, indicating that UAV systems can be used in banana plantations to map spatial patterns of fruit yield; (3) Livestock production is the single largest driver of habitat loss, and both livestock and feedstock production are increasing in developing biodiverse tropical countries. Reducing global animal product consumption should therefore be at the forefront of strategies aimed at reducing biodiversity loss; (4) Removing livestock from global pasture lands and instead utilizing the biomass production could produce enough energy to meet 100% of the electricity, gasoline, and diesel needs of over 40 countries with extensive grassland ecosystems, primarily in tropical developing countries.^

The Maintenance and Consequences of a Low Quality Diet in Poecilia Latipinna

The adaptive significance of herbivory in nature is not well understood. In order to document the conditions that select for an herbivorous feeding habit, we must first understand how such a diet is maintained, and the consequences of doing so. A few studies have begun to reveal mechanisms of maintaining herbivory (i.e. selective feeding, diet mixing, etc.) and the associated life history responses (i.e. growth, reproduction, etc.) in terrestrial and marine systems; however, studies of this kind are underrepresented in the freshwater literature. In this study, I use the sailfin molly (Poecilia latipinna) as a model organism to examine diet selectivity and the effects of an herbivorous diet on growth. To study food selectivity, sailfin mollies were fed either disturbed or intact periphyton mats from one of three localities within the Everglades (Water Conservation Area 3B, the Gap, or Chekika). Mats are structured with palatable algal species (i.e. greens and diatoms) comprising the inner components of the mat, and unpalatable species (i.e. cyanobacteria) comprising the outer edges. Fish gut contents were analyzed for each treatment and periphyton locality. Results suggest that when provided access to the inner components of the mats, fish preferentially eat more palatable algae. In a second experiment, effects of an herbivorous diet were examined using neonate sailfin mollies. Fish were fed either commercial food flakes, commercial algae flakes, or ground periphyton, and growth rate was measured weekly, from birth to 21 days. Fish fed the commercial diets grew at a faster rate and reached a larger final size than those fed periphyton. These results suggest that a periphyton diet is limited in nutritional elements compared to a pure algae diet and herbivorous organisms feeding upon it may experience negative effects on growth. By studying the costs and benefits of herbivory in a freshwater system, this paper contributes to a larger study of the question of why herbivory would evolve as an adaptation when seemingly inefficient compared to carnivorous and omnivorous diets.

Managing small-scale commercial fisheries for adaptive capacity: Insights from dynamic social-ecological drivers of change in Monterey Bay

Globally, small-scale fisheries (SSFs) are driven by climate, governance, and market factors of social-ecological change, presenting both challenges and opportunities. The ability of small-scale fishermen and buyers to adapt to changing conditions allows participants to survive economic or environmental disturbances and to benefit from optimal conditions. This study presented here identifies key large-scale factors that drive SSFs in California to shift focus among targets and that dictate long-term trends in landings. We use Elinor Ostrom’s Social-Ecological System (SES) framework to apply an interdisciplinary approach when identifying potential factors and when understanding the complex dynamics of these fisheries. We analyzed the interactions among Monterey Bay SSFs over the past four decades since the passage of the Magnuson Stevens Fisheries Conservation and Management Act of 1976. In this region, the Pacific sardine (Sardinops sagax), northern anchovy (Engraulis mordax), and market squid (Loligo opalescens) fisheries comprise a tightly linked system where shifting focus among fisheries is a key element to adaptive capacity and reduced social and ecological vulnerability. Using a cluster analysis of landings, we identified four modes from 1974 to 2012 that were dominated by squid, sardine, anchovy, or lacked any dominance, enabling us to identify external drivers attributed to a change in fishery dominance during seven distinct transition points. Overall, we show that market and climate factors drive the transitions among dominance modes. Governance phases most dictated long-term trends in landings and are best viewed as a response to changes in perceived biomass and thus a proxy for biomass. Our findings suggest that globally, small-scale fishery managers should consider enabling shifts in effort among fisheries and retaining existing flexibility, as adaptive capacity is a critical determinant for social and ecological resilience.

Plant biogeography and conservation on a tropical island: Isla del Coco, Costa Rica

Isla del Coco (Cocos Island) is a small volcanic island located in the Pacific 500 km west of Costa Rica. Three collecting trips to Isla del Coco, in addition to herbarium research, were completed in order to assess the floristic diversity of the island. The current flora of Isla del Coco contains 262 plant species of which 37 (19.4%) are endemic. This study reports 58 species as new to the island. Seventy-one species (27.1%) were identified as introduced by humans. In addition, five potentially invasive plant species are identified. Seven vegetation types are identified on the island: bayshore, coastal cliff, riparian, low elevation humid forest, high elevation cloud forest, landslide and islet. ^ The biogeographic affinities of the native and endemic species are with Central America/northern South America and to a lesser extent, the Caribbean. Endemic species in the genus Epidendrum were investigated to determine whether an insular radiation event had produced two species found on Isla del Coco. Phylogenetic analysis of the internal transcribed spacer (ITS) of nuclear ribosomal DNA was not able to disprove that the endemic species in this genus are not sister species. Molecular biogeographic analyses of ITS sequence data determined that the Isla del Coco endemic species in the genera Epidendrum, Pilea and Psychotria are most closely related to Central American/northern South American taxa. No biogeographical links were found between the floras of Isla del Coco and the Galápagos Islands. ^ The native and endemic plant diversity of Isla del Coco is threatened with habitat degradation by introduced pigs and deer, and to a lesser extent, by exotic plant species. The IUCN Red List and RAREplants criteria were used to assess the extinction threat for the 37 endemic plant taxa found on the island. All of the endemic species are considered threatened with extinction at the Critically Endangered (CR) by the IUCN criteria or either CR or Endangered (EN) using RAREplants methodology. ^

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.