Effects of light quantity and quality on early seedling development in the red mangrove Rhizophora mangle L

Seedlings of the red mangrove, Rhizophora mangle L., were grown under light conditions differing in both photosynthetic photon flux density (PPFD) and spectral quality (red:far-red ratio, R:FR). During the first 8 mo of development, parameters of stem, leaf, and root growth were affected by PPFD. Significant responses to lowered R:FR, however, were limited to internode extension. The results are moderately indicative of a strategy to persist in shade, but illustrate the complexity of light responses and suggest that precise categorization as shade-tolerant or -intolerant may be unbefitting for this species at this particular stage of development.

Factors affecting the nodulation and growth of tropical woody legume seedlings

This study surveys the occurrence of nodulation in woody legume species in Panamá and Costa Rica, describes nodule and root characteristics, and researches host-bacteria specificity, nodulation potential of soils, and the effects of light, added nitrogen, and rhizobia and VA mycorrhizal fungi inoculation on seedling growth. I examined 83 species in 37 genera and found 80% to be nodulated. Percent nodulated species in the Caesalpinioideae, Mimosoideae, and Papilionoideae was 17, 95, and 86, respectively, with no correlation between nodule morphology and tribal classification. Nodules formed mainly at root branch points which supports epidermal breaks as an important rhizobia infection route. More non-nodulated than nodulated species had root hairs. Several species emitted volatile sulfur-containing compounds, including the toxic compound ethylmercaptan, from roots, germinating seeds, and other tissues. These emissions may have an allelopathic action against pathogens, predators, or other plants. In contrast to the general non-specificity of most legumes for rhizobia, Mimosa pigra L. was highly specific and only nodulated in flooded soils. This species' specificity, combined with a limited occurrence of its root nodule bacteria may limit its natural distribution, but its spread as an invasive weed is facilitated when fill material from rivers is deposited in other areas. ^ An experimental light level of 1.5% of full sun completely inhibited seedling nodulation, as do similar naturally low levels in forest understory. In the forest, trees and seedlings were not nodulated. in some soils with suspected high N content. For six experimental species, added N progressively increased seedling growth while decreasing nodule biomass; at the highest level of added N nodulation was completely suppressed. Species and individuals showed variation in nodule biomass at high N applications which may indicate an opportunity for genetic selection for optimal N acquisition. Rhizobia inoculation had a small positive effect on seedling shoot growth, but VA mycorrhiza inoculation overwhelmingly increased seedling size, biomass, and leaf mineral concentration. In lowland tropical forest, VA mycorrhizal colonization appears indispensable for legume nodulation because of the fungus' ability to supply P in deficient soils. This requirement makes the legume-rhizobia-mycorrhiza association obligately tripartite. ^

Characterizations of the major coral diseases of the Philippines: Ulcerative white spot disease and novel growth anomalies of Porites

Coral reefs are in decline worldwide and coral disease is a significant contributing factor. However, etiologies of coral diseases are still not well understood. In contrast with the Caribbean, extremely little is known about coral diseases in the Philippines. In 2005, off Southeast Negros Island, Philippines, I investigated relationships between environmental parameters and prevalence of the two most common coral diseases, ulcerative white spot (UWS) and massive Porites growth anomalies (MPGAs). Samples were collected along a disease prevalence gradient 40.5 km long. Principal component analyses showed prevalence of MPGAs was positively correlated with water column nitrogen, organic carbon of surface sediments, and colony density. UWS was positively correlated with water column phosphorus. This is the first quantitative evidence linking anthropogenically-impacted water and sediment to a higher prevalence of these diseases. Histological and cytological alterations were investigated by comparing tissues from two distinct types of MPGA lesions (types 1 and 2) and healthy coral using light and electron microscopy. Skeletal abnormalities and sloughing, swelling, thinning, and loss of tissues in MPGAs resembled tissues exposed to bacterial or fungal toxins. Both lesion types had decreases in symbiotic zooxanthellae, which supply nutrients to corals. Notable alterations included migrations of chromophore cells (amoebocytes) (1) nocturnally to outer epithelia to perform wound-healing, including plugging gaps and secreting melanin in degraded tissues, and (2) diurnally to the interior of the tissue possibly to prevent shading zooxanthellae in order to maximize photosynthate production. Depletion of melanin (active in wound healing) in type 2 lesions suggested type 2 tissues were overtaxed and less stable. MPGAs contained an abundance of endolithic fungi and virus-like particles, which may result from higher nutrient levels and play roles in disease development. Swollen cells and mucus frequently blocked gastrovascular canals (GVCs) in MPGAs. Type 1 lesions appeared to compensate for impeded flow of wastes and nutrients through these canals with proliferation of new GVCs, which were responsible for the observed thickened tissues. In contrast, type 2 tissues were thin and more degraded. Dysplasia and putative neoplasia were also observed in MPGAs which may result from the tissue regeneration capacity being overwhelmed.

Growth and gas exchange responses of Brazilian pepper (Schinus terebinthifolius) and native South Florida species to salinity

Schinus terebinthifolius Raddi (Schinus) is an invasive exotic species widely found in disturbed and native communities of Florida. This species has been shown to displace native species as well as alter community structure and function. The purpose of this study was to determine if the growth and gas exchange patterns of Schinus, under differing salinity conditions, were different from native species. Two native upland glycophytic species (Rapanea punctata and Randia aculeata) and two native mangrove species (Rhizophora mangle and Laguncularia racemosa) were compared with the exotic. Overall, the exotics morphologic changes and gas exchange patterns were most similar to R. mangle. Across treatments, increasing salinity decreased relative growth rate (RGR), leaf area ratio (LAR) and specific leaf area (SLA) but did not affect root/shoot ratios (R:S). Allocation patterns were however significantly different among species. The largest proportion of Schinus biomass was allocated to stems (47%), resulting in plants that were generally taller than the other species. Schinus also had the highest SLA and largest total leaf area of all species. This meant that the exotic, which was taller and had thinner leaves, was potentially able to maintain photosynthetic area comparable to native species. Schinus response patterns show that this exotic exhibits some physiological tolerance for saline conditions. Coupled with its biomass allocation patterns (more stem biomass and large area of thin leaves), the growth traits of this exotic potentially provide this species an advantage over native plants in terms of light acquisition in a brackish forested ecosystem.

Characterizations of the Major Coral Diseases of the Philippines: Ulcerative White Spot Disease and Novel Growth Anomalies of Porites

Coral reefs are in decline worldwide and coral disease is a significant contributing factor. However, etiologies of coral diseases are still not well understood. In contrast with the Caribbean, extremely little is known about coral diseases in the Philippines. In 2005, off Southeast Negros Island, Philippines, I investigated relationships between environmental parameters and prevalence of the two most common coral diseases, ulcerative white spot (UWS) and massive Porites growth anomalies (MPGAs). Samples were collected along a disease prevalence gradient 40.5 km long. Principal component analyses showed prevalence of MPGAs was positively correlated with water column nitrogen, organic carbon of surface sediments, and colony density. UWS was positively correlated with water column phosphorus. This is the first quantitative evidence linking anthropogenically-impacted water and sediment to a higher prevalence of these diseases. Histological and cytological alterations were investigated by comparing tissues from two distinct types of MPGA lesions (types 1 and 2) and healthy coral using light and electron microscopy. Skeletal abnormalities and sloughing, swelling, thinning, and loss of tissues in MPGAs resembled tissues exposed to bacterial or fungal toxins. Both lesion types had decreases in symbiotic zooxanthellae, which supply nutrients to corals. Notable alterations included migrations of chromophore cells (amoebocytes) (1) nocturnally to outer epithelia to perform wound-healing, including plugging gaps and secreting melanin in degraded tissues, and (2) diurnally to the interior of the tissue possibly to prevent shading zooxanthellae in order to maximize photosynthate production. Depletion of melanin (active in wound healing) in type 2 lesions suggested type 2 tissues were overtaxed and less stable. MPGAs contained an abundance of endolithic fungi and virus-like particles, which may result from higher nutrient levels and play roles in disease development. Swollen cells and mucus frequently blocked gastrovascular canals (GVCs) in MPGAs. Type 1 lesions appeared to compensate for impeded flow of wastes and nutrients through these canals with proliferation of new GVCs, which were responsible for the observed thickened tissues. In contrast, type 2 tissues were thin and more degraded. Dysplasia and putative neoplasia were also observed in MPGAs which may result from the tissue regeneration capacity being overwhelmed.

Seawater carbonate chemistry, growth rate and PIC and POC production during experiments with Emiliania huxleyi (B92/11), 2011

The coccolithophore Emiliania huxleyi was cultured under a broad range of carbonate chemistry conditions to distinguish the effects of individual carbonate system parameters on growth, primary production, and calcification. In the first experiment, alkalinity was kept constant and the fugacity of CO2(fCO2) varied from 2 to 600 Pa (1Pa ~ 10 µatm). In the second experiment, pH was kept constant (pHfree = 8) with fCO2 varying from 4 to 370 Pa. Results of the constant-alkalinity approach revealed physiological optima for growth, calcification, and organic carbon production at fCO2 values of ~20Pa, ~40 Pa, and ~80 Pa, respectively. Comparing this with the constant-pH approach showed that growth and organic carbon production increased similarly from low to intermediate CO2 levels but started to diverge towards higher CO2 levels. In the high CO2 range, growth rates and organic carbon production decreased steadily with declining pH at constant alkalinity while remaining consistently higher at constant pH. This suggests that growth and organic carbon production rates are directly related to CO2 at low (sub-saturating) concentrations, whereas towards higher CO2 levels they are adversely affected by the associated decrease in pH. A pH dependence at high fCO2 is also indicated for calcification rates, while the key carbonate system parameter determining calcification at low fCO2 remains unclear. These results imply that key metabolic processes in coccolithophores have their optima at different carbonate chemistry conditions and are influenced by different parameters of the carbonate system at both sides of the optimum.

Effects of in situ CO2 enrichment on structural characteristics, photosynthesis, and growth of the Mediterranean seagrass Posidonia oceanica

Seagrass is expected to benefit from increased carbon availability under future ocean acidification. This hypothesis has been little tested by in situ manipulation. To test for ocean acidification effects on seagrass meadows under controlled CO2/pH conditions, we used a Free Ocean Carbon Dioxide Enrichment (FOCE) system which allows for the manipulation of pH as continuous offset from ambient. It was deployed in a Posidonia oceanica meadow at 11 m depth in the Northwestern Mediterranean Sea. It consisted of two benthic enclosures, an experimental and a control unit both 1.7 m**3, and an additional reference plot in the ambient environment (2 m**2) to account for structural artifacts. The meadow was monitored from April to November 2014. The pH of the experimental enclosure was lowered by 0.26 pH units for the second half of the 8-month study. The greatest magnitude of change in P. oceanica leaf biometrics, photosynthesis, and leaf growth accompanied seasonal changes recorded in the environment and values were similar between the two enclosures. Leaf thickness may change in response to lower pH but this requires further testing. Results are congruent with other short-term and natural studies that have investigated the response of P. oceanica over a wide range of pH. They suggest any benefit from ocean acidification, over the next century (at a pH of 7.7 on the total scale), on Posidonia physiology and growth may be minimal and difficult to detect without increased replication or longer experimental duration. The limited stimulation, which did not surpass any enclosure or seasonal effect, casts doubts on speculations that elevated CO2 would confer resistance to thermal stress and increase the buffering capacity of meadows.

Seawater carbonate chemistry and growth rate of Emiliania huxleyi in lab experiment

Predicting the impacts of environmental change on marine organisms, food webs, and biogeochemical cycles presently relies almost exclusively on short-term physiological studies, while the possibility of adaptive evolution is often ignored. Here, we assess adaptive evolution in the coccolithophore Emiliania huxleyi, a well-established model species in biological oceanography, in response to ocean acidification. We previously demonstrated that this globally important marine phytoplankton species adapts within 500 generations to elevated CO2. After 750 and 1000 generations, no further fitness increase occurred, and we observed phenotypic convergence between replicate populations. We then exposed adapted populations to two novel environments to investigate whether or not the underlying basis for high CO2-adaptation involves functional genetic divergence, assuming that different novel mutations become apparent via divergent pleiotropic effects. The novel environment "high light" did not reveal such genetic divergence whereas growth in a low-salinity environment revealed strong pleiotropic effects in high CO2 adapted populations, indicating divergent genetic bases for adaptation to high CO2. This suggests that pleiotropy plays an important role in adaptation of natural E. huxleyi populations to ocean acidification. Our study highlights the potential mutual benefits for oceanography and evolutionary biology of using ecologically important marine phytoplankton for microbial evolution experiments.

Rising CO2 and increased light exposure synergistically reduce marine primary productivity

Carbon dioxide and light are two major prerequisites of photosynthesis. Rising CO2 levels in oceanic surface waters in combination with ample light supply are therefore often considered stimulatory to marine primary production. Here we show that the combination of an increase in both CO2 and light exposure negatively impacts photosynthesis and growth of marine primary producers. When exposed to CO2 concentrations projected for the end of this century, natural phytoplankton assemblages of the South China Sea responded with decreased primary production and increased light stress at light intensities representative of the upper surface layer. The phytoplankton community shifted away from diatoms, the dominant phytoplankton group during our field campaigns. To examine the underlying mechanisms of the observed responses, we grew diatoms at different CO2 concentrations and under varying levels (5-100%) of solar radiation experienced by the phytoplankton at different depths of the euphotic zone. Above 22-36% of incident surface irradiance, growth rates in the high-CO2-grown cells were inversely related to light levels and exhibited reduced thresholds at which light becomes inhibitory. Future shoaling of upper-mixed-layer depths will expose phytoplankton to increased mean light intensities. In combination with rising CO2 levels, this may cause a widespread decline in marine primary production and a community shift away from diatoms, the main algal group that supports higher trophic levels and carbon export in the ocean.

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Data compilation of dinoflagellates growth rate, grazing rate and gross gowth efficiency from field and labratory experiments

The present data compilation includes dinoflagellates growth rate, grazing rate and gross growth efficiency determined either in the field or in laboratory experiments. From the existing literature, we synthesized all data that we could find on dinoflagellates. Some sources might be missing but none were purposefully ignored. We did not include autotrophic dinoflagellates in the database, but mixotrophic organisms may have been included. This is due to the large uncertainty about which taxa are mixotrophic, heterotrophic or symbiont bearing. Field data on microzooplankton grazing are mostly comprised of grazing rate using the dilution technique with a 24h incubation period. Laboratory grazing and growth data are focused on pelagic ciliates and heterotrophic dinoflagellates. The experiment measured grazing or growth as a function of prey concentration or at saturating prey concentration (maximal grazing rate). When considering every single data point available (each measured rate for a defined predator-prey pair and a certain prey concentration) there is a total of 801 data points for the dinoflagellates, counting experiments that measured growth and grazing simultaneously as 1 data point.

Data compilation of ciliates growth rate, grazing rate and gross gowth efficiency from field and labratory experiments

The present data compilation includes ciliates growth rate, grazing rate and gross growth efficiency determined either in the field or in laboratory experiments. From the existing literature, we synthesized all data that we could find on cilliate. Some sources might be missing but none were purposefully ignored. Field data on microzooplankton grazing are mostly comprised of grazing rate using the dilution technique with a 24h incubation period. Laboratory grazing and growth data are focused on pelagic ciliates and heterotrophic dinoflagellates. The experiment measured grazing or growth as a function of prey concentration or at saturating prey concentration (maximal grazing rate). When considering every single data point available (each measured rate for a defined predator-prey pair and a certain prey concentration) there is a total of 1485 data points for the ciliates, counting experiments that measured growth and grazing simultaneously as 1 data point.

Epitaxial growth of visible to infra-red transparent conducting In2O3 nanodot dispersions and reversible charge storage as a Li-ion battery anode

Unique bimodal distributions of single crystal epitaxially grown In2O3 nanodots on silicon are shown to have excellent IR transparency greater than 87% at IR wavelengths up to 4 μm without sacrificing transparency in the visible region. These broadband antireflective nanodot dispersions are grown using a two-step metal deposition and oxidation by molecular beam epitaxy, and backscattered diffraction confirms a dominant (111) surface orientation. We detail the growth of a bimodal size distribution that facilitates good surface coverage (80%) while allowing a significant reduction in In2O3 refractive index. This unique dispersion offers excellent surface coverage and three-dimensional volumetric expansion compared to a thin film, and a step reduction in refractive index compared to bulk active materials or randomly porous composites, to more closely match the refractive index of an electrolyte, improving transparency. The (111) surface orientation of the nanodots, when fully ripened, allows minimum lattice mismatch strain between the In2O3 and the Si surface. This helps to circumvent potential interfacial weakening caused by volume contraction due to electrochemical reduction to lithium, or expansion during lithiation. Cycling under potentiodynamic conditions shows that the transparent anode of nanodots reversibly alloys lithium with good Coulombic efficiency, buffered by co-insertion into the silicon substrate. These properties could potentially lead to further development of similarly controlled dispersions of a range of other active materials to give transparent battery electrodes or materials capable of non-destructive in situ spectroscopic characterization during charging and discharging.

MOVPE growth and characterization of Al(Ga)N and InAlN/AlGaN quantum wells for UV LED applications

The study of III-nitride materials (InN, GaN and AlN) gained huge research momentum after breakthroughs in the production light emitting diodes (LEDs) and laser diodes (LDs) over the past two decades. Last year, the Nobel Prize in Physics was awarded jointly to Isamu Akasaki, Hiroshi Amano and Shuji Nakamura for inventing a new energy efficient and environmental friendly light source: blue light-emitting diode (LED) from III-nitride semiconductors in the early 1990s. Nowadays, III-nitride materials not only play an increasingly important role in the lighting technology, but also become prospective candidates in other areas, for example, the high frequency (RF) high electron mobility transistor (HEMT) and photovoltaics. These devices require the growth of high quality III-nitride films, which can be prepared using metal organic vapour phase epitaxy (MOVPE). The main aim of my thesis is to study and develop the growth of III-nitride films, including AlN, u-AlGaN, Si-doped AlGaN, and InAlN, serving as sample wafers for fabrication of ultraviolet (UV) LEDs, in order to replace the conventional bulky, expensive and environmentally harmful mercury lamp as new UV light sources. For application to UV LEDs, reducing the threading dislocation density (TDD) in AlN epilayers on sapphire substrates is a key parameter for achieving high-efficiency AlGaNbased UV emitters. In Chapter 4, after careful and systematic optimisation， a working set of conditions, the screw and edge type dislocation density in the AlN were reduced to around 2.2×108 cm-2 and 1.3×109 cm-2 , respectively, using an optimized three-step process, as estimated by TEM. An atomically smooth surface with an RMS roughness of around 0.3 nm achieved over 5×5 µm 2 AFM scale. Furthermore, the motion of the steps in a one dimension model has been proposed to describe surface morphology evolution, especially the step bunching feature found under non-optimal conditions. In Chapter 5, control of alloy composition and the maintenance of compositional uniformity across a growing epilayer surface were demonstrated for the development of u-AlGaN epilayers. Optimized conditions (i.e. a high growth temperature of 1245 °C) produced uniform and smooth film with a low RMS roughness of around 2 nm achieved in 20×20 µm 2 AFM scan. The dopant that is most commonly used to obtain n-type conductivity in AlxGa1-xN is Si. However, the incorporation of Si has been found to increase the strain relaxation and promote unintentional incorporation of other impurities (O and C) during Si-doped AlGaN growth. In Chapter 6, reducing edge-type TDs is observed to be an effective appoach to improve the electric and optical properties of Si-doped AlGaN epilayers. In addition, the maximum electron concentration of 1.3×1019 cm-3 and 6.4×1018 cm-3 were achieved in Si-doped Al0.48Ga0.52N and Al0.6Ga0.4N epilayers as measured using Hall effect. Finally, in Chapter 7, studies on the growth of InAlN/AlGaN multiple quantum well (MQW) structures were performed, and exposing InAlN QW to a higher temperature during the ramp to the growth temperature of AlGaN barrier (around 1100 °C) will suffer a significant indium (In) desorption. To overcome this issue, quasi-two-tempeature (Q2T) technique was applied to protect InAlN QW. After optimization, an intense UV emission from MQWs has been observed in the UV spectral range from 320 to 350 nm measured by room temperature photoluminescence.

Site controlled red-yellow-green light emitting InGaN quantum discs on nano-tipped GaN rods

We report a method of growing site controlled InGaN multiple quantum discs (QDs) at uniform wafer scale on coalescence free ultra-high density (>80%) nanorod templates by metal organic chemical vapour deposition (MOCVD). The dislocation and coalescence free nature of the GaN space filling nanorod arrays eliminates the well-known emission problems seen in InGaN based visible light sources that these types of crystallographic defects cause. Correlative scanning transmission electron microscopy (STEM), energy-dispersive X-ray (EDX) mapping and cathodoluminescence (CL) hyperspectral imaging illustrates the controlled site selection of the red, yellow and green (RYG) emission at these nano tips. This article reveals that the nanorod tips' broad emission in the RYG visible range is in fact achieved by manipulating the InGaN QD's confinement dimensions, rather than significantly increasing the In%. This article details the easily controlled method of manipulating the QDs dimensions producing high crystal quality InGaN without complicated growth conditions needed for strain relaxation and alloy compositional changes seen for bulk planar GaN templates.