Development of molecular approaches to assess the diversity and abundance of marine nematodes assemblages for assessment of Good Environmental Status of the estuarine and marine ecosystems

In Europe, the concerns with the status of marine ecosystems have increased, and the Marine Directive has as main goal the achievement of Good Environmental Status (GES) of EU marine waters by 2020. Molecular tools are seen as promising and emerging approaches to improve ecosystem monitoring, and have led ecology into a new era, representing perhaps the most source of innovation in marine monitoring techniques. Benthic nematodes are considered ideal organisms to be used as biological indicator of natural and anthropogenic disturbances in aquatic ecosystems underpinning monitoring programmes on the ecological quality of marine ecosystems, very useful to assess the GES of the marine environment. dT-RFLP (directed Terminal-Restriction Fragment Length Polymorphism) allows to assess the diversity of nematode communities, but also allows studying the functioning of the ecosystem, and combined with relative real-time PCR (qPCR), provides a high-throughput semi-quantitative characterization of nematode communities. These characteristics make the two molecular tools good descriptors for the good environmental status assessment. The main aim of this study is to develop and optimize the dT-RFLP and qPCR in Mira estuary (SW coast, Portugal). A molecular phylogenetic analysis of marine and estuarine nematodes is being performed combining morphological and molecular analysis to evaluate the diversity of free-living marine nematodes in Mira estuary. After morphological identification, barcoding of 18S rDNA and COI genes are being determined for each nematode species morphologically identified. So far we generated 40 new sequences belonging to 32 different genus and 17 families, and the study has shown a good degree of concordance between traditional morphology-based identification and DNA sequences. These results will improve the assessment of marine nematode diversity and contribute to a more robust nematode taxonomy. The DNA sequences are being used to develop the dT-RFLP with the ability to easily process large sample numbers (hundreds and thousands), rather than typical of classical taxonomic or low throughput molecular analyses. A preliminary study showed that the digest enzymes used in dT-RFLP for terrestrial assemblages separated poorly the marine nematodes at taxonomic level for functional group analysis. A new digest combination was designed using the software tool DRAT (Directed Terminal Restriction Analysis Tool) to distinguished marine nematode taxa. Several solutions were provided by DRAT and tested empirically to select the solution that cuts most efficiently. A combination of three enzymes and a single digest showed to be the best solution to separate the different clusters. Parallel to this, another tool is being developed to estimate the population size (qPCR). An improvement in qPCR estimation of gene copy number using an artificial reference is being performed for marine nematodes communities to quantify the abundance. Once developed, it is proposed to validate both methodologies by determining the spatial and temporal variability of benthic nematodes assemblages across different environments. The application of these high-throughput molecular approaches for benthic nematodes will improve sample throughput and their implementation more efficient and faster as indicator of ecological status of marine ecosystems.

Study of different atmospheric environments associated to storms development in the Madeira Island

The study aims to improve the understanding about different atmospheric environments leading to the development of storms associated with heavy precipitation in Madeira Island. For this purpose, four main goals have been considered: 1) To document the synoptic and mesoscale environments associated with heavy precipitation. 2) To characterize surface precipitation patterns that affected the island during some periods of significant accumulated precipitation using numerical modelling. 3) To study the relationship between surface precipitation patterns and mesoscale environments. 4) To highlight how the PhD findings obtained in the first three goals can be translated into an operational forecast context. Concerning the large scale environment, precipitation over the island was favoured by weather systems (e.g, mesoscale convective systems and low pressure systems), as well as by the meridional transport of high amount of moisture from a structure denominated as “Atmospheric River”. The tropical origin of this moisture is underscored, however, their impact on the precipitation in Madeira was not so high during the 10 winter seasons [2002 – 2012] studied. The main factor triggering heavy precipitation events over the island is related to the local orography. The steep terrain favours orographically-induced stationary precipitation over the highlands, although maximum of precipitation at coastal region may be produced by localized blocking effect. These orographic precipitating systems presented different structures, associated with shallow and deep convection. Essentially, the study shows that the combination of airflow dynamics, moist content, and orography is the major mechanism that produces precipitation over the island. These factors together with the event duration act to define the regions of excessive precipitation. Finally, the study highlights two useful points for the operational sector, regarding the meridional water vapour transport and local effects causing significant precipitation over the Island; RESUMO: O estudo procura melhorar o entendimento sobre os diferentes ambientes atmosféricos que favorecem o desenvolvimento de tempestades associadas com precipitação intensa na ilha da Madeira. Nesse sentido foram definidos quatro objetivos: 1) Documentar os ambientes sinópticos e de mesoescala associados com precipitação intensa; 2) Caracterizar padrões de precipitação na superfície, em eventos de elevada precipitação acumulada, utilizando modelação numérica; 3) Estudar as relações entre os padrões de precipitação e ambientes de mesoescala; 4) Mostrar como tais resultados podem ser utilizados num contexto operacional de previsão do tempo. Em relação a ambientes de larga escala, verificou-se que a ocorrência de eventos de precipitação intensa sobre a ilha foi favorecida por sistemas meteorológicos, assim como pelo transporte meridional de humidade por meio de estruturas atualmente denominadas Rios atmosféricos. Neste último caso é de destacar a origem tropical de humidade, no entanto, o seu impacto na precipitação sobre a Madeira durante os 10 invernos estudados [2002-2012] não foi tão elevada. O principal fator que favorece os eventos de precipitação intensa está relacionado com a orografia local. O terreno complexo da ilha favorece a ocorrência de precipitação estacionária induzida orograficamente sobre as terras mais altas, embora a precipitação nas zonas costeiras possa ser produzida por um efeito localizado de bloqueio. Estes sistemas orográficos precipitantes apresentaram diferentes estruturas, associados a convecção pouco profunda e profunda. O estudo mostra que a combinação entre as características do escoamento, a quantidade de humidade, e a orografia são os condimentos essenciais para o desenvolvimento da precipitação sobre a ilha, atuando de maneira a definir as regiões de precipitação excessiva. Por fim, o estudo destaca dois pontos que podem ser úteis na previsão do tempo operacional, ligados a larga escala e aos efeitos locais, os quais podem levar ao desenvolvimento de tempestades e precipitação intensa sobre a ilha.

Leaf water potential and sap flow as indicators of water stress in Crimson ‘seedless’ grapevines under different irrigation strategies

Vitis vinifera L. cv. Crimson Seedless is a late season red table grape developed in 1989, with a high market value and increasingly cultivated under protected environments to extend the availability of seedless table grapes into the late fall. The purpose of this work was to evaluate leaf water potential and sap flow as indicators of water stress in Crimson Seedless vines under standard and reduced irrigation strategy, consisting of 70 % of the standard irrigation depth. Additionally, two sub-treatments were applied, consisting of normal irrigation throughout the growing season and a short irrigation induced stress period between veraison and harvest. Leaf water potential measurements coherently signaled crop-available water variations caused by different irrigation treatments, suggesting that this plant-based method can be reliably used to identify water-stress conditions. The use of sap flow density data to establish a ratio based on a reference ‘well irrigated vine’ and less irrigated vines can potentially be used to signal differences in the transpiration rates, which may be suitable for improving irrigation management strategies while preventing undesirable levels of water stress. Although all four irrigation strategies resulted in the production of quality table grapes, significant differences (p ≤ 0.05) were found in both berry weight and sugar content between the standard irrigation and reduced irrigation treatments. Reduced irrigation increased slightly the average berry size as well as sugar content and technical maturity index. The 2-week irrigation stress period had a negative effect on these parameters.

Leaf water potential and sap flow as indicators of water stress in Crimson 'seedless' grapevines under different irrigation strategies

Abstract Vitis vinifera L. cv. Crimson Seedless is a late season red table grape developed in 1989, with a high market value and increasingly cultivated under protected environments to extend the availability of seedless table grapes into the late fall. The purpose of this work was to evaluate leaf water potential and sap flow as indicators of water stress in Crimson Seedless vines under standard and reduced irrigation strategy, consisting of 70 % of the standard irrigation depth. Additionally, two sub-treatments were applied, consisting of normal irrigation throughout the growing season and a short irrigation induced stress period between veraison and harvest. Leaf water potential measurements coherently signaled crop-available water variations caused by different irrigation treatments, suggesting that this plant-based method can be reliably used to identify water-stress conditions. The use of sap flow density data to establish a ratio based on a reference ‘well irrigated vine’ and less irrigated vines can potentially be used to signal differences in the transpiration rates, which may be suitable for improving irrigation management strategies while preventing undesirable levels of water stress. Although all four irrigation strategies resulted in the production of quality table grapes, significant differences (p ≤ 0.05) were found in both berry weight and sugar content between the standard irrigation and reduced irrigation treatments. Reduced irrigation increased slightly the average berry size as well as sugar content and technical maturity index. The 2-week irrigation stress period had a negative effect on these parameters.