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 By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived.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.

Effect of the environment on condition and quality of cultured blue mussels (Mytilus edulis) with reference to culture depth and post-harvest practices

The condition and quality of cultured blue mussels (Mytilus edulis) are affected by various environmental characteristics including temperature, salinity, food concentration, composition and year-to-year variability, waves, tides, and currents. Mussels are a keystone species in the ecosystem, affecting the surrounding environment through filtration, biodeposition and nutrient recycling. This study evaluated the effects of culture depth and post-harvest handling on cultured blue mussels in Newfoundland, Canada. Depth was examined over two years; three shallow water (5 m depth) and three deep water sites (15 m depth) were compared for environmental characteristics, mussel physiological stress response, growth, and biochemical composition. The area examined presented complex hydrodynamic characteristics; deep water sites appeared to be located more often near or within the pycnocline than shallow water sites. Deep water sites presented lower temperatures than shallow sites from spring to fall. Physiological stress response varied seasonally, but was unaffected by culture depth. In Year 1 shallow and deep water mussels presented similar growth, while in Year 2 deep water mussels showed better final condition. Lipid and glycogen showed seasonal variation, but no significant differences between shallow and deep water were noted. Fatty acid profiles showed a higher content of omega-3s PUFA in deep water sites at the end of Year 2. Under extreme weather conditions, deep water appeared to provide a more stable environment for mussel growth than shallow water. Harvested mussels were kept under ambient live-holding conditions for one month during the fall, winter, and spring seasons. They were compared to freshly harvested mussels for condition, biochemical profile and palatability. A progressive loss of dry tissue weight and an increase in water content were shown over the holding period during the fall and spring seasons, when compared to field controls. The biochemical analysis suggested seasonal changes; differences in triacylglycerol content were found in the spring season when compared with controls. The palatability data indicated that the panellists were unable to determine a difference between mussels kept in holding and those freshly harvested from the site. This study presents new knowledge for mussel farming, especially in terms of environmental interactions and deep water culture.

Morphometrics of seagrasses at species level, Moreton Bay, Australia determined from core samples collected in 2012-2013

Seagrass meadows are important marine carbon sinks, yet they are threatened and declining worldwide. Seagrass management and conservation requires adequate understanding of the physical and biological factors determining carbon content in seagrass sediments. Here, we identified key factors that influence carbon content in seagrass meadows across several environmental gradients in Moreton Bay, SE Queensland. Sampling was conducted in two regions: (1) Canopy Complexity, 98 sites on the Eastern Banks, where seagrass canopy structure and species composition varied while turbidity was consistently low; and (2) Turbidity Gradient, 11 locations across the entire bay, where turbidity varied among sampling locations. Sediment organic carbon content and seagrass structural complexity (shoot density, leaf area, and species specific characteristics) were measured from shallow sediment and seagrass biomass cores at each location, respectively. Environmental data were obtained from empirical measurements (water quality) and models (wave height). The key factors influencing carbon content in seagrass sediments were seagrass structural complexity, turbidity, water depth, and wave height. In the Canopy Complexity region, carbon content was higher for shallower sites and those with higher seagrass structural complexity. When turbidity varied along the Turbidity Gradient, carbon content was higher at sites with high turbidity. In both regions carbon content was consistently higher in sheltered areas with lower wave height. Seagrass canopy structure, water depth, turbidity, and hydrodynamic setting of seagrass meadows should therefore be considered in conservation and management strategies that aim to maximize sediment carbon content.

Estimating density of a rare and cryptic high-mountain Galliform species, the Buff-throated Partridge Tetraophasis szechenyii

Estimates of abundance or density are essential for wildlife management and conservation. There are few effective density estimates for the Buff-throated Partridge Tetraophasis szechenyii, a rare and elusive high-mountain Galliform species endemic to western China. In this study, we used the temporary emigration N-mixture model to estimate density of this species, with data acquired from playback point count surveys around a sacred area based on indigenous Tibetan culture of protection of wildlife, in Yajiang County, Sichuan, China, during April–June 2009. Within 84 125-m radius points, we recorded 53 partridge groups during three repeats. The best model indicated that detection probability was described by covariates of vegetation cover type, week of visit, time of day, and weather with weak effects, and a partridge group was present during a sampling period with a constant probability. The abundance component was accounted for by vegetation association. Abundance was substantially higher in rhododendron shrubs, fir-larch forests, mixed spruce-larch-birch forests, and especially oak thickets than in pine forests. The model predicted a density of 5.14 groups/km², which is similar to an estimate of 4.7 – 5.3 groups/km² quantified via an intensive spot-mapping effort. The post-hoc estimate of individual density was 14.44 individuals/km², based on the estimated mean group size of 2.81. We suggest that the method we employed is applicable to estimate densities of Buff-throated Partridges in large areas. Given importance of a mosaic habitat for this species, local logging should be regulated. Despite no effect of the conservation area (sacred) on the abundance of Buff-throated Partridges, we suggest regulations linking the sacred mountain conservation area with the official conservation system because of strong local participation facilitated by sacred mountains in land conservation.

You and I: The Effects of Intra- and Inter-Species Interactions on Microbial Biofilms, Growth, and Morphology

Humanity is shaped by its relationships with microbes. From bacterial infections to the production of biofuels, industry and health often hinge on our control of microbial populations. Understanding the physiological and genetic basis of their behaviors is therefore of the highest importance. To this end I have investigated the genetic basis of plastic adhesion in Saccharomyces cerevisiae, the mechanistic and evolutionary dynamics of mixed species biofilms with Escherichia coli and S. cerevisiae, and the induction of filamentation in E. coli. Using a bulk segregant analysis on experimentally evolved populations, I detected 28 genes that are likely to mediate plastic adhesion in S. cerevisiae. With a variety of imaging and culture manipulation techniques, I found that particular strains of E. coli are capable of inducing flocculation and macroscopic biofilm formation via coaggregation with yeast. I also employed experimental evolution and microbial demography techniques to find that selection for mixed species biofilm association leads to lower fecundity in S. cerevisiae. Using culture manipulation and imaging techniques, I also found that E. coli are capable of inducing a filamentous phenotype with a secreted signal that has many of the qualities of a quorum sensing molecule.

Multi-proxy records of Two-Yurts Lake

Within the scope of Russian-German palaeoenvironmental research, Two-Yurts Lake (TYL, Dvuh-Yurtochnoe in Russian) was chosen as the main scientific target area to decipher Holocene climate variability on Kamchatka. The 5x2 km large and 26 m deep lake is of proglacial origin and situated on the eastern flank of Sredinny Ridge at the northwestern end of the Central Kamchatka Valley, outside the direct influence of active volcanism. Here, we present results of a multi-proxy study on sediment cores, spanning about the last 7000 years. The general tenor of the TYL record is an increase in continentality and winter snow cover in conjunction with a decrease in temperature, humidity, and biological productivity after 5000-4500 cal yrs BP, inferred from pollen and diatom data and the isotopic composition of organic carbon. The TYL proxy data also show that the late Holocene was punctuated by two colder spells, roughly between 4500 and 3500 cal yrs BP and between 1000 and 200 cal yrs BP, as local expressions of the Neoglacial and Little Ice Age, respectively. These environmental changes can be regarded as direct and indirect responses to climate change, as also demonstrated by other records in the regional terrestrial and marine realm. Long-term climate deterioration was driven by decreasing insolation, while the short-term climate excursions are best explained by local climatic processes. The latter affect the configuration of atmospheric pressure systems that control the sources as well as the temperature and moisture of air masses reaching Kamchatka.

Effects of hypercapnia on aspects of feeding, nutrition, and growth in the edible sea urchin Lytechinus variegatus held in culture

Land-based aquaculture facilities experience occasional hypercapnic conditions due to the accumulation of the metabolic waste product carbon dioxide. Pre-gonadal Lytechinus variegatus (horizontal diameter=20 mm) were exposed to control (608 µatm pCO2, pH 8.1) or hypercapnic conditions (1738 µatm pCO2, pH 7.7) in synthetic seawater for 14 weeks. Sea urchins exposed to hypercapnic conditions exhibited significantly slower growth (reduced dry matter production), primarily due to reduced test production. Higher fecal production rates and lower ash absorption efficiency (%) in individuals exposed to hypercapnic conditions suggest the ability to process or retain dietary carbonates may have been affected. Significant increases in neutral lipid storage in the gut and increased soluble protein storage in the gonads of individuals exposed to hypercapnic conditions suggest alterations in nutrient metabolism and storage. Furthermore, organic production and energy allocation increased in the lantern of those individuals exposed to hypercapnic conditions. These results suggest chronic exposure to hypercapnic conditions alters nutrient allocation to organ systems and functions, leading to changes in somatic and reproductive production.

The effect of a reduction of nitrogen and phosphorus to eutrophic and mesotrophic conditions towards silver nanoparticle (AgNP) on freshwater green algae species

We investigated the sensitivity of algae towards silver nanoparticles with OECD test medium and lower nutrient concentrations under standard test conditions to improve comparability and to exclude any other confounding factor aside nutrient levels. Two unicellular freshwater microalgae Desmodesmus subspicatus and Raphidocelis subcapitata were chosen due to their status as standard test organisms for the algae growth inhibition test and the response to changes in nutrient supply was compared. The original medium was used as the reference (standard). For the other four media, the amount of either nitrogen or phosphorus in the medium was lowered from half (50%) to one-fourth (25 %) of that of the OECD guideline, resulting in the following media: 50% N, 25% N, 50% P and 25% P medium. As test substance, the OECD reference material NM-300K was used. For this reason, the characterization of AgNP was done using DLS and Absorption spectra (UV/vis). Actual silver concentrations and ionic silver concentrations were measured at the highest test concentration used (100 µg Ag L-1) in R. subcapitata treatments only to reduce the number of samples. All tests were run according to the OECD guideline 201 with sterilized 50 mL cell culture flask. Each medium was tested using the test conditions for culturing with 3 replicates. Test concentrations for both algae species were 0, 25, 50 and 100 µg Ag L-1 for OECD, 50% P and 25% P while for both N reductions, the silver concentrations were 0, 10, 25 and 100 µg Ag L-1. Samples for determining the algal density were taken at every 24 h.

Organisational and systems factors impacting on patient safety in acute care organisations: lessons from four multi-site research studies

Background Patient safety is concerned with preventable harm in healthcare, a subject that became a focus for study in the UK in the late 1990s. How to improve patient safety, presented both a practical and a research challenge in the early 2000s, leading to the eleven publications presented in this thesis. Research question The overarching research question was: What are the key organisational and systems factors that impact on patient safety, and how can these best be researched? Methods Research was conducted in over 40 acute care organisations in the UK and Europe between 2006 and 2013. The approaches included surveys, interviews, documentary analysis and non-participant observation. Two studies were longitudinal. Results The findings reveal the nature and extent of poor systems reliability and its effect on patient safety; the factors underpinning cases of patient harm; the cultural issues impacting on safety and quality; and the importance of a common language for quality and safety across an organisation. Across the publications, nine key organisational and systems factors emerged as important for patient safety improvement. These include leadership stability; data infrastructure; measurement capability; standardisation of clinical systems; and creating an open and fair collective culture where poor safety is challenged. Conclusions and contribution to knowledge The research presented in the publications has provided a more complete understanding of the organisation and systems factors underpinning safer healthcare. Lessons are drawn to inform methods for future research, including: how to define success in patient safety improvement studies; how to take into account external influences during longitudinal studies; and how to confirm meaning in multi-language research. Finally, recommendations for future research include assessing the support required to maintain a patient safety focus during periods of major change or austerity; the skills needed by healthcare leaders; and the implications of poor data infrastructure.

The invasion risk in the Pacific Northwest of two closely related grass species in the Genus Cortaderia

Thesis (Master's)--University of Washington, 2016-08

The effect of ecological changes in Lake Victoria on the present trophic characteristics of Oreochromis niloticus in relation to the species' role as a stabilizing factor of biomanipulation

The Lake Victoria ecosystem has experienced such a profound ecological change that Oreochromis niloticus - an introduced species, is the only important cichlid (out of the original 250 + spp) left in the lake. It is the basis of an important commercial fishery which is intensely exploited by sophisticated methods. An investigation of its feeding habits at present indicates that the species could also playa major role in the energy flux of the lake. Fisheries management in Lake Victoria will thus require multi-disciplinary studies which reflect a total ecosystem approach.

A new species of gall midge (Diptera: Cecidomyiidae) feeding on ornamental Cordyline fruticosa(Asparagaceae) in Australia

Larvae of an undescribed gall midge were found feeding on leaves and stems within leaf sheaths and between leaf blades of potted plants of Cordyline fruticosa (Asparagaceae) in a production nursery in Queensland. The following varieties of the host plant were infested: Apple Blossom', Glauca', Kilauea', Negra', Pink Diamond, 'Purple Prince' and Willy's Gold'. The new species, Dasineura cordylineaeKolesik sp. nov., is described and its cytochrome oxidase unit I mitochondrial gene segment is sequenced. The new species is the first known gall midge feeding on a plant species of the genus Cordyline. Orange larvae induce oval shallow swellings on the leaf and stem tissue, which becomes necrotised during the later stage of larval feeding. Necrotic areas remain visible to the end of leaves' lives and decrease the market value of the plants. In the production nursery investigated, the lesions caused by the gall midge provided an entry for a fungal infection by Fusarium sp. inflicting further injury to plants. Larvae of the new species were preyed on by larvae of Gaurax sp. (Diptera: Chloropidae). This is the first worldwide record of Chloropidae preying on Cecidomyiidae.

Exploring complex chemical systems: insights from mass spectrometry, electrochemistry and continuous cell culture

The work presented herein covers a broad range of research topics and so, in the interest of clarity, has been presented in a portfolio format. Accordingly, each chapter consists of its own introductory material prior to presentation of the key results garnered, this is then proceeded by a short discussion on their significance. In the first chapter, a methodology to facilitate the resolution and qualitative assessment of very large inorganic polyoxometalates was designed and implemented employing ion-mobility mass spectrometry. Furthermore, the potential of this technique for ‘mapping’ the conformational space occupied by this class of materials was demonstrated. These claims are then substantiated by the development of a tuneable, polyoxometalate-based calibration protocol that provided the necessary platform for quantitative assessments of similarly large, but unknown, polyoxometalate species. In addition, whilst addressing a major limitation of travelling wave ion mobility, this result also highlighted the potential of this technique for solution-phase cluster discovery. The second chapter reports on the application of a biophotovoltaic electrochemical cell for characterising the electrogenic activity inherent to a number of mutant Synechocystis strains. The intention was to determine the key components in the photosynthetic electron transport chain responsible for extracellular electron transfer. This would help to address the significant lack of mechanistic understanding in this field. Finally, in the third chapter, the design and fabrication of a low-cost, highly modular, continuous cell culture system is presented. To demonstrate the advantages and suitability of this platform for experimental evolution investigations, an exploration into the photophysiological response to gradual iron limitation, in both the ancestral wild type and a randomly generated mutant library population, was undertaken. Furthermore, coupling random mutagenesis to continuous culture in this way is shown to constitute a novel source of genetic variation that is open to further investigation.

Variation of cutting rooting ability in cultivated and wild species of Macadamia

In Australia, macadamia trees are commonly propagated by germinating rootstock seed and grafting when seedlings reach a suitable size. The production of grafted trees is a protracted and complex process, however, propagation of macadamia via cuttings represents a simpler and faster method of multiplication. Macadamias have traditionally proven difficult to propagate from cuttings, and while recent developments in the process have improved success rates, substantial variation in rooting ability between cultivars and species has been reported. The cultivar 'Beaumont' (Macadamia integrifolia × M. tetraphylla) is commonly propagated by cutting for use as a rootstock, and is relatively easy to strike while other cultivars are more difficult. There is speculation that Hawaiian cultivars are more difficult to strike from cuttings than Australian cultivars due to species and genetic composition. In this experiment, cuttings of 32 genotypes were evaluated for rooting ability. Each genotype's species profile was estimated using historical data, and used to determine species effects on survival (percentage) and rooting ability (rating 0-2). M. jansenii (100%), M. tetraphylla (84%) and M. integrifolia/tetraphylla hybrids (79%) had the highest success rates while M. integrifolia (54%) and M. ternifolia (43%) had the lowest survival. Rooting ability of M. jansenii (1.75) was significantly higher than M. ternifolia (0.49) but not significantly higher than M. tetraphylla × M. integrifolia with (1.09), M. tetraphylla (1.03) or M. integrifolia (0.88).

Harvesting and Collection of Animal Forest Species

The harvest and trade of corals and other benthic organisms from the world’s shallow tropical reefs is a lucrative industry that can have positive socioeconomic benefits for communities while supplying the increasing demand specimens for aquaria and curios. For most countries, this trade has historically been almost entirely unregulated. More recently, in response to concerns about the rapid decline of some reefs in the face of anthropogenic and natural pressures, as well as indications of depletions and even localized extinctions of some species caused by harvesting, there have been attempts to improve the sustainability of the industry. Both developing and developed countries face different impediments to this reform, the most pressing and common of which is the lack of reliable data on world trade through CITES. Thereafter, differences in the processes through which reform can be implemented are based principally on the length of the supply chain from collection to export, the degree of industry stewardship, and resourcing. The coral collection fishery in Queensland, Australia, provides an example where continual improvements in reporting and risk assessments and adopting a comanagement approach are delivering better adaptive management of the resource, although the on-ground sustainability benefits of this approach are still to be tested. A simpler approach to sustainable use of coral is to favor the replacement of wild harvested specimens with those bred or grown entirely in an aquaculture facility (as opposed to merely collected and then grown out in culture). Yet there are major impediments to this change, including the dependence of many public aquaria on the same sources as the hobbyist community, difficulties of culturing some species in captivity, and infrastructure costs. Nevertheless, this approach will likely play an important part in reef conservation efforts in the future.