Microbiology of sugar-rich environments: Diversity, ecology and system constraints

Microbial habitats that contain an excess of carbohydrate in the form of sugar are widespread in the microbial biosphere. Depending on the type of sugar, prevailing water activity and other substances present, sugar-rich environments can be highly dynamic or relatively stable, osmotically stressful, and/or destabilizing for macromolecular systems, and can thereby strongly impact the microbial ecology. Here, we review the microbiology of different high-sugar habitats, including their microbial diversity and physicochemical parameters, which act to impact microbial community assembly and constrain the ecosystem. Saturated sugar beet juice and floral nectar are used as case studies to explore the differences between the microbial ecologies of low and higher water-activity habitats respectively. Nectar is a paradigm of an open, dynamic and biodiverse habitat populated by many microbial taxa, often yeasts and bacteria such as, amongst many others, Metschnikowia spp. and Acinetobacter spp., respectively. By contrast, thick juice is a relatively stable, species-poor habitat and is typically dominated by a single, xerotolerant bacterium (Tetragenococcus halophilus). A number of high-sugar habitats contain chaotropic solutes (e.g. ethyl acetate, phenols, ethanol, fructose and glycerol) and hydrophobic stressors (e.g. ethyl octanoate, hexane, octanol and isoamyl acetate), all of which can induce chaotropicity-mediated stresses that inhibit or prevent multiplication of microbes. Additionally, temperature, pH, nutrition, microbial dispersion and habitat history can determine or constrain the microbiology of high-sugar milieux. Findings are discussed in relation to a number of unanswered scientific questions.

Water structure and chaotropicity: their uses, abuses and biological implications

The concept of "water structure" has been invoked to explain all manner of aqueous phenomena. Here we look at the origins of this tendency to understand solute hydration in terms of structural changes in bulk water, and consider the validity of one particular example: the classification of small solutes as chaotropic or kosmotropic, and the putative relation of this terminology to notions of structure-making and structure-breaking in the solvent. We doubt whether complex phenomena such as Hofmeister and osmolyte effects on macromolecules can be understood simply on the basis of a change in solvent structure. Rather, we argue that chaotropicity, if understood in the original sense, arises from the activities that solutes exert on macromolecular systems, as well as from deviations of solvation water from bulk-like behaviour. If applied judiciously, chaotropicity remains a potent, biologically pertinent parameter useful for classifying and understanding solution phenomena in all types of living system.

Development of a slurry continuous flow reactor for photocatalytic treatment of industrial waste water

The water treatment capability of a novel photocatalytic slurry reactor was investigated using methylene blue (MB) as a model pollutant in an aqueous suspension. A pellet TiO ₂ catalyst was employed and this freed the system from the need of filtration of catalyst following photocatalysis. This configuration combines the high surface area contact of catalyst with pollutant of the slurry reactor and also offers a high illumination of catalyst by its unique array of weir-like baffles. In this work, the batch adsorption of MB from aqueous solution (10μM) onto the TiO ₂ catalyst was studied, adsorption isotherms and kinetics were determined from the experimental data. Complete degradation of MB was achieved within 60 min illumination with various loadings of catalyst (30-200 g L ^-1). A modest catalyst loading (30 g L ^-1) achieved 98% degradation within 60 min of irradiation. Experimental results indicate that this novel reactor configuration has a high effective mass transfer rate and UV light penetration characteristics. 

A new sensory organ in "primitive" molluscs (Polyplacophora Lepidopleurida), and its context in the nervous system of chitons

Introduction: Chitons (Polyplacophora) are molluscs considered to have a simple nervous system without cephalisation. The position of the class within Mollusca is the topic of extensive debate and neuroanatomical characters can provide new sources of phylogenetic data as well as insights into the fundamental biology of the organisms. We report a new discrete anterior sensory structure in chitons, occurring throughout Lepidopleurida, the order of living chitons that retains plesiomorphic characteristics.

Results: The novel "Schwabe organ" is clearly visible on living animals as a pair of streaks of brown or purplish pigment on the roof of the pallial cavity, lateral to or partly covered by the mouth lappets. We describe the histology and ultrastructure of the anterior nervous system, including the Schwabe organ, in two lepidopleuran chitons using light and electron microscopy. The oesophageal nerve ring is greatly enlarged and displays ganglionic structure, with the neuropil surrounded by neural somata. The Schwabe organ is innervated by the lateral nerve cord, and dense bundles of nerve fibres running through the Schwabe organ epithelium are frequently surrounded by the pigment granules which characterise the organ. Basal cells projecting to the epithelial surface and cells bearing a large number of ciliary structures may be indicative of sensory function. The Schwabe organ is present in all genera within Lepidopleurida (and absent throughout Chitonida) and represents a novel anatomical synapomorphy of the clade.

Conclusions: The Schwabe organ is a pigmented sensory organ, found on the ventral surface of deep-sea and shallow water chitons; although its anatomy is well understood, its function remains unknown. The anterior commissure of the chiton oesophagial nerve ring can be considered a brain. Our thorough review of the chiton central nervous system, and particularly the sensory organs of the pallial cavity, provides a context to interpret neuroanatomical homology and assess this new sense organ.

Net energy analysis of a solar combi system with Seasonal Thermal Energy Store

EU targets require nearly zero energy buildings (NZEB) by 2020. However few monitored examples exist of how NZEB has been achieved in practise in individual residential buildings. This paper provides an example of how a low-energy building (built in 2006), has achieved nearly zero energy heating through the addition of a solar domestic hot water and space heating system (“combi system”) with a Seasonal Thermal Energy Store (STES). The paper also presents a cumulative life cycle energy and cumulative life cycle carbon analysis for the installation based on the recorded DHW and space heating demand in addition to energy payback periods and net energy ratios. In addition, the carbon and energy analysis is carried out for four other heating system scenarios including hybrid solar thermal/PV systems in order to obtain the optimal system from a carbon efficiency perspective.

Management and Control of Water Supply Systems

The fast increase in the energy’s price has brought a growing concern about the highly expensive task of transporting water. By creating an hydraulic model of the Water Supply System’s (WSS) network and predicting its behaviour, it is possible to take advantage of the energy’s tariffs, reducing the total cost on pumping activities. This thesis was developed, in association with a technology transfer project called the E-Pumping. It focuses on finding a flexible supervision and control strategy, adaptable to any existent Water Supply System (WSS), as well as forecasting the water demand on a time period chosen by the end user, so that the pumping actions could be planned to an optimum schedule, that minimizes the total operational cost. The OPC protocol, associated to a MySQL database were used to develop a flexible tool of supervision and control, due to their adaptability to function with equipments from various manufacturers, being another integrated modular part of the E-Pumping project. Furthermore, in this thesis, through the study and performance tests of several statistical models based on time series, specifically applied to this problem, a forecasting tool adaptable to any station, and whose model parameters are automatically refreshed at runtime, was developed and added to the project as another module. Both the aforementioned modules were later integrated with an Graphical User Interface (GUI) and installed in a pilot application at the ADDP’s network. The implementation of this software on WSSs across the country will reduce the water supply companies’ running costs, improving their market competition and, ultimately, lowering the water price to the end costumer.

Combining sampling, profiling, remote sensing and modelling to efficiently monitoring estuarine and coastal water quality

Monitoring of coastal and estuarine water quality has been traditionally performed by sampling with subsequent laboratory analysis. This has the disadvantages of low spatial and temporal resolution and high cost. In the last decades two alternative techniques have emerged to overcome this drawback: profiling and remote sensing. Profiling using multi-parameter sensors is now in a commercial stage. It can be used, tied to a boat, to obtain a quick “picture” of the system. The spatial resolution thus increases from single points to a line coincident with the boat track. The temporal resolution however remains unchanged since campaigns and resources involved are basically the same. The need for laboratory analysis was reduced but not eliminated because parameters like nutrients, microbiology or metals are still difficult to obtain with sensors and validation measurements are still needed. In the last years the improvement in satellite resolution has enabled its use for coastal and estuarine water monitoring. Although spatial coverage and resolution of satellite images in the present is already suitable to coastal and estuarine monitoring, temporal resolution is naturally limited to satellite passages and cloud cover. With this panorama the best approach to water monitoring is to integrate and combine data from all these sources. The natural tools to perform this integration are numerical models. Models benefit from the different sources of data to obtain a better calibration. After calibration they can be used to extend spatially and temporally the methods resolution. In Algarve (South of Portugal) a monitoring effort using this approach is being undertaken. The monitoring effort comprises five different locations including coastal waters, estuaries and coastal lagoons. The objective is to establish the base line situation to evaluate the impact of Waste Water Treatment Plants design and retrofitting. The field campaigns include monthly synoptic profiling, using an YSI 6600 multi-parameter system, laboratory analysis and fixed stations. The remote sensing uses ENVISAT\MERIS Level 2 Full Resolution data. This data is combined and used with the MOHID modelling system to obtain an integrate description of the systems. The results show the limitations of each method and the ability of the modelling system to integrate the results and to produce a comprehensive picture of the system.

Advanced monitoring of South Portugal water bodies towards WFD

The challenge on implementation of the EU Water Framework Directive (WFD) fosters the development of new monitoring methods and approaches. It is now commonly accepted that the use of classical monitoring campaigns in discrete point is not sufficient to fully assess and describe a water body. Due to this the WFD promote the use of modelling techniques in surface waters to assist all phases of the process, from characterisation and establishment of reference conditions to identification of pressures and assessment of impact. The work presented in this communication is based on these principles. A classical monitoring of the water status of the main transitional water bodies of Algarve (south of Portugal) is combined with advanced in situ water profiling and hydrodynamic, water quality and ecological modelling of the systems to build a complete description of its state. This approach extends spatially and temporally the resolution of the classical point sampling. The methodology was applied during a 12 month program in Ria Formosa coastal lagoon, the Guadiana estuary and the Arade estuary. The synoptic profiling uses an YSI 6600 EDS multi-parameter system attached to a boat and a GPS receiver to produce monthly synoptic maps of the systems. This data extends the discrete point sampling with laboratory analysis performed monthly in several points of each water body. The point sampling is used to calibrate the profiling system and to include variables, such as nutrients, not measured by the sensors. A total of 1427 samplings were performed for physical and chemical parameters, chlorophyll and microbiologic contamination in the water column. This data is used to drive the hydrodynamic, transport and ecological modules of the MOHID water modelling system (www.mohid.com), enabling an integrate description of the water column.

EU water framework directive: will the nitrate load reduction from diffuse sources produce the same results in all estuaries?

The impact of urban waste-water and non-point nitrate discharges in estuarine and near-shore coastal waters are analyzed. The study is focused on the effects of applying the European directives 91/271/EEC and 91/676/EEC to these systems. 4 Portuguese estuaries and two coastal lagoons with different characteristics are studied. A modelling system is applied and calibrated in each system. Three nitrate load scenarios are examined. It is shown that the morphologic and hydrodynamic characteristics of the domain largely control the ecological processes in these systems. The primary production limitation factors are split into “biologic” and “hydrodynamic” components. The physical limitation due to hydrodynamic and residence time is the most important factor. The combined limitation of “biologic” factors (temperature, light and nutrients availability) control productivity only in the systems where physical limitation is not important.

Valuing water in irrigated agriculture and fisheries in a reservoir of Sri Lanka

Dissertação de Mestrado, Gestão da Água e da Costa, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2007

A system approach framework to the management of lake Baringo, Kenya

Dissertação de Mestrado, Gestão da Água e da Costa, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2010

Understanding the importance of sediments to water ouality in coastal shallow lagoons

The undesirable enrichment of water by nutrients may be a problem, especially in areas with restricted exchange with the sea. The tidal regime flushes the system and contributes for the removal of phytoplankton, favouring phytobenthos as the target of enhanced nutrients. Water samples were collected during the years of 2006 and 2007-08 for nutrients, chlorophyll a and dissolved oxygen. Sediment sample s were also collected for pore water nutrients and benthic chlorophyll a. From comparison with previous work, a decrease in the nitrogen concentration in the water column can be pointed out, which may indicate an improvement of the water quality. Pore water DAIN represents approximately 75% of the total DAIN of the whole lagoon. Benthic chlorophyll a concentrations were much larger than in the water column, representing around 99% of the total chlorophyll existent in the lagoon. Benthic microalgae play a relevant role in this system and therefore standard monitoring programs of the WFD, which do not consider this component, may fail to track nutrient-driven changes in primary producers. Dissolved oxygen concentration could be near critical levels during the summer (early in the morning), especially in the inner channels.

Acoustic oceanographic buoy telemetry system: an ‘advanced’ sonobuoy that meets acoustic rapid environmental assessment requirements

The Acoustic Oceanographic Buoy (AOB) Telemetry System has been designed to meet acoustic rapid environmental assessment requirements. It uses a standard institute of Electrical and Electronics Engineers 802.11 wireless local area network (WLAN) to integrate the air radio network (RaN) and a hydrophone array and acoustic source to integrate the underwater acoustic network (AcN). It offers advantages including local data storage, dedicated signal processing, and global positioning system (GPS) timing and localization. The AOB can also be integrated with other similar systems, due to its WLAN transceivers, to form a flexible network and perform on-line high speed data transmissions. The AOB is a reusable system that requires less maintenance and can also work as a salt-water plug-and-play system at sea as it is designed to operate in free drifting mode. The AOB is also suitable for performing distributed digital signal processing tasks due to its digital signal processor facility.

An autonomous system for ocean acoustic tomography

Vertical line arrays (VLA) are a widely used apparatus in underwater acoustics with applications in sonar prediction, underwater communications and acoustic tomography, among others. Recent developments in digital electronics and communications allow for off-the-shelf development of VLA systems, with a large number of embedded acoustic and non-acoustic sensors able to fulfill application requirements, as opposed to single or few receiver configurations available until only a few years ago. Very often, the flexibility in water column sampling is achieved by splitting the VLA into modules that can be assembled according to the application. Such systems can be deployed and recovered from small vessels with a shorthanded crew, and make it possible for research labs with reduced budgets and operational means (ships and manpower) to gain control over the whole development process, from data acquisition to post-processing.

Continental surface water and energy budgets in the XX and XXI centuries

Tese de doutoramento, Ciências Geofísicas e da Geoinformação (Meteorologia), Universidade de Lisboa, Faculdade de Ciências, 2015