Selection of a network of large lakes and reservoirs suitable for global environmental change analysis using Earth Observation

The GloboLakes project, a global observatory of lake responses to environmental change, aims to exploit current satellite missions and long remote-sensing archives to synoptically study multiple lake ecosystems, assess their current condition, reconstruct past trends to system trajectories, and assess lake sensitivity to multiple drivers of change. Here we describe the selection protocol for including lakes in the global observatory based upon remote-sensing techniques and an initial pool of the largest 3721 lakes and reservoirs in the world, as listed in the Global Lakes and Wetlands Database. An 18-year-long archive of satellite data was used to create spatial and temporal filters for the identification of waterbodies that are appropriate for remote-sensing methods. Further criteria were applied and tested to ensure the candidate sites span a wide range of ecological settings and characteristics; a total 960 lakes, lagoons, and reservoirs were selected. The methodology proposed here is applicable to new generation satellites, such as the European Space Agency Sentinel-series.

Assessing the utility of geospatial technologies to investigate environmental change within lake systems

Over 50% of the world's population live within 3. km of rivers and lakes highlighting the on-going importance of freshwater resources to human health and societal well-being. Whilst covering c. 3.5% of the Earth's non-glaciated land mass, trends in the environmental quality of the world's standing waters (natural lakes and reservoirs) are poorly understood, at least in comparison with rivers, and so evaluation of their current condition and sensitivity to change are global priorities. Here it is argued that a geospatial approach harnessing existing global datasets, along with new generation remote sensing products, offers the basis to characterise trajectories of change in lake properties e.g., water quality, physical structure, hydrological regime and ecological behaviour. This approach furthermore provides the evidence base to understand the relative importance of climatic forcing and/or changing catchment processes, e.g. land cover and soil moisture data, which coupled with climate data provide the basis to model regional water balance and runoff estimates over time. Using examples derived primarily from the Danube Basin but also other parts of the World, we demonstrate the power of the approach and its utility to assess the sensitivity of lake systems to environmental change, and hence better manage these key resources in the future.

Synecology in soft sediment bivalves: the influence of parasites, physiological processes, and environmental stressors on health and disease

Ecosystem goods and services provided by estuarine and near coastal regions are being increasingly recognised for their immense value, as is the biodiversity in these areas and these near coastal communities have been identified as sentinels of climate change also. Population structure and reproductive biology of two bivalve molluscs, Cerastoderma edule and, Mytilus edulis were assessed at two study sites over a 16-month study period. Following an anomalously harsh winter, advancement of spawning time was observed in both species. Throughout Ireland and Europe the cockle has experienced mass surfacings in geographically distinct regions, and a concurrent study of cockles was undertaken to explore this phenomenon. Surfaced and buried cockles were collected on a monthly basis and their health compared. Age was highlighted as a source of variation between dying and healthy animals with a parasite threshold being reached possibly around age three. Local factors dominated when looking at the cause of surfacing at each site. The health of mussels was explored too on a temporal and seasonal basis in an attempt to assess what constitutes a healthy organism. In essence external drivers can tip the balance between “acceptable” levels of infection where the mussel can still function physiologically and “unacceptable” where prevalence and intensity of infection can result in physiological impairment at the individual and population level. Synecological studies of intertidal ecosystems are lacking, so all bivalves encountered during the sampling were assessed in terms of population structure, reproduction, and health. It became clear, that some parasites might specialize on one host species while others are not so specific in host choice. Furthermore the population genetics of the cockle, its parasite Meiogymnophallus minutus, and its hyperparasite Unikaryon legeri were examined too. A small nucleotide polymorphism was detected upon comparison of Ireland and Morocco.

The importance of interaction strength for food web dynamics and ecosystem functioning

Global biodiversity is eroding at an alarming rate, through a combination of anthropogenic disturbance and environmental change. Ecological communities are bewildering in their complexity. Experimental ecologists strive to understand the mechanisms that drive the stability and structure of these complex communities in a bid to inform nature conservation and management. Two fields of research have had high profile success at developing theories related to these stabilising structures and testing them through controlled experimentation. Biodiversity-ecosystem functioning (BEF) research has explored the likely consequences of biodiversity loss on the functioning of natural systems and the provision of important ecosystem services. Empirical tests of BEF theory often consist of simplified laboratory and field experiments, carried out on subsets of ecological communities. Such experiments often overlook key information relating to patterns of interactions, important relationships, and fundamental ecosystem properties. The study of multi-species predator-prey interactions has also contributed much to our understanding of how complex systems are structured, particularly through the importance of indirect effects and predator suppression of prey populations. A growing number of studies describe these complex interactions in detailed food webs, which encompass all the interactions in a community. This has led to recent calls for an integration of BEF research with the comprehensive study of food web properties and patterns, to help elucidate the mechanisms that allow complex communities to persist in nature. This thesis adopts such an approach, through experimentation at Lough Hyne marine reserve, in southwest Ireland. Complex communities were allowed to develop naturally in exclusion cages, with only the diversity of top trophic levels controlled. Species removals were carried out and the resulting changes to predator-prey interactions, ecosystem functioning, food web properties, and stability were studied in detail. The findings of these experiments contribute greatly to our understanding of the stability and structure of complex natural communities.

Genetic analysis of bacteriophages from clinical and environmental samples

Bacteriophages, viruses infecting bacteria, are uniformly present in any location where there are high numbers of bacteria, both in the external environment and the human body. Knowledge of their diversity is limited by the difficulty to culture the host species and by the lack of the universal marker gene present in all viruses. Metagenomics is a powerful tool that can be used to analyse viral communities in their natural environments. The aim of this study was to investigate diverse populations of uncultured viruses from clinical (a sputum of patient with cystic fibrosis, CF) and environmental samples (a sludge from a dairy food wastewater treatment plant) containing rich bacterial populations using genetic and metagenomic analyses. Metagenomic sequencing of viruses obtained from these samples revealed that the majority of the metagenomic reads (97-99%) were novel when compared to the NCBI protein database using BLAST. A large proportion of assembled contigs were assignable as novel phages or uncharacterised prophages, the next largest assignable group being single-stranded eukaryotic virus genomes. Sputum from a cystic fibrosis patient contained DNA typical of phages of bacteria that are traditionally involved in CF lung infections and other bacteria that are part of the normal oral flora. The only eukaryotic virus detected in the CF sputum was Torque Teno virus (TTV). A substantial number of assigned sequences from dairy wastewater could be affiliated with phages of bacteria that are typically found in the soil and aquatic environments, including wastewater. Eukaryotic viral sequences were dominated by plant pathogens from the Geminiviridae and Nanoviridae families, and animal pathogens from the Circoviridae family. Antibiotic resistance genes were detected in both metagenomes suggesting phages could be a source for transmissible antimicrobial resistance. Overall, diversity of viruses in the CF sputum was low, with 89 distinct viral genotypes predicted, and higher (409 genotypes) in the wastewater. Function-based screening of a metagenomic library constructed from DNA extracted from dairy food wastewater viruses revealed candidate promoter sequences that have ability to drive expression of GFP in a promoter-trap vector in Escherichia coli. The majority of the cloned DNA sequences selected by the assay were related to ssDNA circular eukaryotic viruses and phages which formed a minority of the metagenome assembly, and many lacked any significant homology to known database sequences. Natural diversity of bacteriophages in wastewater samples was also examined by PCR amplification of the major capsid protein sequences, conserved within T4-type bacteriophages from Myoviridae family. Phylogenetic analysis of capsid sequences revealed that dairy wastewater contained mainly diverse and uncharacterized phages, while some showed a high level of similarity with phages from geographically distant environments.