A Contribution to the Ecological Knowledge of the Atlantic Coastal Wetlands of the Iberian Peninsula, a Fragile Border Between Two Worlds

Programa Oficial de Doutoramento en Ciencia e Tecnoloxía Ambiental . 5006V01[Abstract] Coastal wetlands are ecotones defined by the degree of interaction between terrestrial and marine ecosystems. In this PhD dissertation the hydrochemical conditions of 27 coastal wetlands of the Western Atlantic Iberian Coast (WIAC) and 39 of the Eastern Mediterranean Iberian Coast (EMIC) are compared. Large-scale geographical patterns (lithology and climate) are the main factors determining the water composition, and changes in the ionic composition in the salinity range 1.25 - 2.5 (4) ‰ determine the decisive breakpoint for the terrestrial and marine biological communities. These ecosystems are inhabited by singular taxa, such as the diatoms Nitzschia varelae, a new brackish species; Synedropsis roundii, which is found for the first time in the atlantic southern European coasts; and Attheya armata, a `surf diatom´ whose proliferations are linked to the sediment-water interface. A detailed biological and geological study of the coastal lake Doniños (NW Iberian), revealed that although at present its nutrient and phytoplankton dynamics is undistinguishable from any continental temperate lake, it showed large differences in its environmental conditions since it formed c. 4.5 ka cal BP after the mid-Holocene sea-level stabilization.[Resumen] Los humedales costeros son ecotonos definidos por el grado de interacción entre los ecosistemas terrestres y marinos. En esta tesis doctoral se comparan las condiciones hidroquímicas de 27 humedales costeros de la Costa Ibérica del Atlántico Occidental (WIAC) y 39 de la Costa Ibérica del Mediterráneo Oriental (EMIC). Los patrones geográficos a gran escala (litología y clima) son los principales factores que determinan la composición del agua, y los cambios en la composición iónica en el rango de salinidad 1.25 – 2.5 (4.0) ‰ determinan el punto de ruptura decisivo para las comunidades biológicas terrestres y marinas. Estos ecosistemas están habitados por taxones singulares, como las diatomeas Nitzschia varelae, una nueva especie salobre; Synedropsis roundii, encontrada por primera vez en las costas atlánticas del sur de Europa; y Attheya armata, una `surf diatom´ cuyas proliferaciones están ligadas a la interfase sedimento-agua. Un detallado estudio biológico y geológico del lago costero de Doniños (NO Ibérico), reveló que aunque en la actualidad su dinámica de nutrientes y fitoplancton es indistinguible de cualquier lago continental templado, mostró grandes diferencias en sus condiciones ambientales desde que se formó c. 4.5 ka cal BP después de la estabilización del nivel del mar en el Holoceno medio.[Resumo] Os humidais costeiros son ecotonos definidos polo grao de interacción entre ecosistemas terrestres e mariños. Nesta tese doutoral compáranse as condicións hidroquímicas de 27 humidais costeiros da costa ibérica do Atlántico occidental (WIAC) e 39 da costa ibérica do Mediterráneo oriental (EMIC). Os patróns xeográficos a gran escala (litoloxía e clima) son os principais factores que determinan a composición da auga e os cambios na composición iónica no intervalo de salinidade 1.25 – 2.5 (4.0) ‰ que determina o punto de ruptura decisivo para as comunidades biolóxicas terrestres e mariñas. Estes ecosistemas están habitados por taxóns únicos, como as diatomeas Nitzschia varelae, unha nova especie salobre; Synedropsis roundii, atopada por primeira vez nas costas atlánticas do sur de Europa; e Attheya armata, unha "diatomea de surf" cuxas proliferacións son debidas a procesos que se producen na interfase sedimento-auga. Un detallado estudo biolóxico e xeolóxico do lago Doniños na costa Ibérica noroeste revelou que, aínda que na actualidade a súa dinámica de nutrientes e fitoplancto non se distingue de ningún lago continental temperado, mostrou grandes diferenzas nas súas condicións ambientais desde o século c. 4,5 ka cal BP despois da estabilización do nivel do mar no Holoceno medio

First Record of a Freshwater Bryozoan Species in Cuba: Plumatella Repens (Linnaeus, 1758) (Phylactolaemata, Bryozoa)

[Abstract] The discovery of Plumatella repens floatoblasts in wetlands of the La Niña Bonita Reservoir and the Ciénaga de Zapata Swamp, Cuba, constitutes the first record of a freshwater bryozoan species on the island and extends the distribution range of the species in the insular Caribbean. Unlike the inland waters of the Lesser Antilles the greater availability of water and lower salinity are likely the main factors that determine the distribution of P. repens in the Greater Antilles

Diversity of Testate Amoebae as an Indicator of the Conservation Status of Peatlands in Southwest Europe

Testate amoebae are one of the most studied groups of microorganisms in Sphagnum peatland ecosystems and, therefore, one of the most reliable bioindicators of their ecological status. Peatland ecosystems are supported by a delicate biogeochemical balance that leads to the formation of peat, one of the main sinks of C, as a result of soil–atmosphere interaction, but currently they are one of the most threatened wetland types at their southern distribution limit. In the European continent, where climatic conditions limit peat formation, they have endured significant anthropic pressure for centuries, and the risk of loss of biodiversity linked to these ecosystems is critical. In addition, peatlands are poorly known ecosystems in the Iberian Peninsula compared with other wetlands; therefore, we have studied the chemical parameters of water and the diversity patterns of testate amoebae in the western Iberian Peninsula to better understand the current status of these ecosystems. The analysis of testate amoeba communities showed an inverse relationship between the diversity and conservation status of these peatlands, both in relation to chemical parameters (i.e., pH, electrical conductivity, phosphates) and to the proportion of anthropized area, with a marked geographical pattern in the degree of anthropogenic disturbanceThis research was made possible thanks to a grant awarded by the Xunta de Galicia (project: INCITE09–200-019-PR) and thanks to the support of “Consolidación e Estructuración 2018 GRC GI-1243-GEMAP, ED431C 2018/32”S

Stratification Strength and Light Climate Explain Variation in Chlorophyll at the Continental Scale in a European Multilake Survey in a Heatwave Summer

[Abstract] To determine the drivers of phytoplankton biomass, we collected standardized morphometric, physical, and biological data in 230 lakes across the Mediterranean, Continental, and Boreal climatic zones of the European continent. Multilinear regression models tested on this snapshot of mostly eutrophic lakes (median total phosphorus [TP] = 0.06 and total nitrogen [TN] = 0.7 mg L⁻¹), and its subsets (2 depth types and 3 climatic zones), show that light climate and stratification strength were the most significant explanatory variables for chlorophyll a (Chl ) variance. TN was a significant predictor for phytoplankton biomass for shallow and continental lakes, while TP never appeared as an explanatory variable, suggesting that under high TP, light, which partially controls stratification strength, becomes limiting for phytoplankton development. Mediterranean lakes were the warmest yet most weakly stratified and had significantly less Chl than Boreal lakes, where the temperature anomaly from the long-term average, during a summer heatwave was the highest (+4°C) and showed a significant, exponential relationship with stratification strength. This European survey represents a summer snapshot of phytoplankton biomass and its drivers, and lends support that light and stratification metrics, which are both affected by climate change, are better predictors for phytoplankton biomass in nutrient-rich lakes than nutrient concentrations and surface temperature.The authors acknowledge COST Action ES 1105 “CYANOCOST – Cyanobacterial blooms and toxins in water resources: Occurrence impacts and management” and COST Action Global Change Biology ES 1201 NETLAKE – Networking Lake Observatories in Europe” for contributing to this study through networking and knowledge sharing with European experts in the field. We acknowledge the members of the Global Lake Ecological Observatory Network (GLEON) for their collaborative spirit and enthusiasm that inspired the grassroots effort of the EMLS. E.M. was supported by a grant from the Swiss State Secretariat for Education, Research and Innovation to Bas Ibelings and by supplementary funding from University of Geneva. We thank Wendy Beekman for the nutrient analysis. We thank Pieter Slot for assisting with the pigment analysis. We thank Dr. Ian Jones for valuable feedback on an earlier version of the manuscript. We thank the Leibniz Institute of Freshwater Ecology and the Aquatic Microbial Ecology Group for logistic and technical support of J. Fonvielle and H.-P. Grossart, and the Leibniz Association for financial support. H.P. was supported by the US National Science Foundation (1840715, 1831096). A.C.’s work was funded by the Spanish Agencia Estatal de Investigacion and EU funds through the project CLIMAWET (CGL2015-69557-R). The collection of data for Lough Erne and Lough Neagh were funded by the Department of Agriculture, Environment and Rural Affairs, Northern Ireland. We are grateful to Kristiina Vuorio from the Freshwater Centre of the Finnish Environment institute for her help in organizing, collecting and analysing samples by the University of Jyväskylä and to Gerald Dörflinger from the Water Development Department of Cyprus for his assistance with the sampling in Cyprus and for granting the CUT team permission to use WDD’s equipment. Finally, we would like to thank the numerous other assistants that helped realizing each local survey. Open access funding provided by Universite de GeneveEstados Unidos. US National Science Foundation; 1831096Estados Unidos. US National Science Foundation; 184071

Diatomeas epilíticas (Bacillariophyceae) de los cursos de agua corriente del NO de la península ibérica (Galicia, España)

A catalog of Bacillariophyceae for the rivers of NW of Spain is made for the first time. It includes a re-examination of the taxa reported in previous publications, taxa cited during the last years of the rivers of the Galicia-Costa Hydrographic Demarcation, and a revision of the taxonomy, in line with the systematic and nomenclature changes, which have occurred mainly in recent years. The epilethic diatoms of the river basins of Galicia-Costa were sampled during the years 2005, 2006, and 2007, in May-June and September. The study was carried out in 41 localities distributed along 31 rivers, samples were taken in upstream and downstream sections. Diatom communities were compared in all upstream sections of these rivers draining from siliceous substrates. We identified 141 taxa of diatoms from the coast of Galicia. In this paper we present 15 new citations for Galicia, two for Spain and three for the Iberian Peninsula, in addition to a new species recently described. The dominant taxa are: Achnanthidium minutissimum, Achnanthes subhudsonis, Karayevia oblongella, Cocconeis placentula var. euglypta, Gomphonema rhombicum, and Navicula minima. Achnanthes subhudsonis was the most abundant species during the spring and summer months. The remaining species showed no relevant changes regardless of the time of year. The results indicate that the river diatoms of Galicia are an important component of the diversity of the ecosystem.Se realiza por primera vez un catálogo de Bacillariophyceae para los ríos del NW de España. Se incluyen un nuevo examen de los táxones recogidos en publicaciones anteriores, datos de táxones citados durante los últimos años de los ríos de la demarcación hidrográfica de Galicia-Costa y una revisión de la taxonomía, en consonancia con los cambios sistemáticos y nomenclaturales, que se han producido sobre todo durante los últimos años. Se estudiaron las diatomeas epilíticas de las cuencas de los ríos de Galicia-Costa entre los años 2005, 2006 y 2007, durante dos temporadas diferentes: mayo-junio y septiembre. El estudio se llevó a cabo en 41 localidades distribuidas a lo largo de 31 ríos, donde se tomaron muestras en tramos aguas arriba y aguas abajo. Las comunidades de diatomeas de estos ríos que drenan de sustratos silíceos fueron comparadas en todos los tramos de aguas arriba. Se identificaron 141 táxones de diatomeas de la costa de Galicia. En este trabajo presentamos 15 nuevas citas para Galicia, dos para España y tres para la Península Ibérica, además de una nueva especie recientemente descrita. Los táxones dominantes son: Achnanthidium minutissimum, Achnanthes subhudsonis, Karayevia oblongella, Cocconeis placentula var. euglypta, Gomphonema rhombicum, y Navicula minima. Achnanthes subhudsonis fue la especie más abundante durante los meses de primavera y verano. Las especies restantes no mostraron cambios pertinentes independientemente de la época del año. Los resultados indican que las diatomeas de los ríos de Galicia son un componente importante de la diversidad del ecosistema

Phycological biodiversity at the Natural Park Serra da Enciña da Lastra (Ourense, Spain)

We have studied the phycological diversity at the Natural Park of Serra da Enciña da Lastra (Ourense, Spain) and present here the algae checklist of the Galir river, the only permanent fluvial course in the area. This geographical zone is a SCI (Site of Community Importance) and is located within an European Nature Reserve belonging to the “Nature 2000” network. Despite its environmental importance there is no previous phycological survey to this study. We collected samples in three points along the river, and measured physical and chemical water parameters (pH, conductivity, temperature, and dissolved oxygen). The checklist includes 88 taxa: 6 Cyanophyta, 4 Rhodophyta, 60 Heterokontophyta (58 Bacillariophyceae, 2 Xantophyceae), 1 Dinophyta, 2 Euglenophyta, and 15 Chlorophyta. Within the Rhodophyta we highlight the presence of Lemanea condensata, as a new record to the Iberian Peninsula. In addition, we have identified 8 new records for Galicia and 14 for OurenseSe ha estudiado la diversidad ficológica del río Galir, el único curso fluvial permanente del Parque Natural Serra da Enciña da Lastra (Orense, España). Es un Lugar de Importancia Comunitaria (LIC) incluido en la red de espacios naturales “Natura 2000”. A pesar de su importancia ambiental, no hay ningún estudio ficológico previo al presente. El catálogo de la flora ficológica incluye táxones recogidos de tres puntos del río y se han tenido en cuenta algunos parámetros físicoquímicos del agua: pH, conductividad, temperatura y oxígeno disuelto. El catálogo florístico incluye 88 táxones: 6 Cyanophyta, 4 Rhodophyta, 60 Heterokontophyta (58 Bacillariophyceae y 2 Xantophyceae), 1 Dinophyta, 2 Euglenophyta y 15 Chlorophyta. Entre las Rhodophyta destaca Lemanea condensata, por ser nueva cita para la Península Ibérica. Además, se han encontrado 8 nuevas citas para Galicia y 14 para la provincia de OrenseThis study was funded by the Consellería de Medio Ambiente e Desenvolvemento Sostible de la Xunta de Galicia (PGIDIT05RFO20002PR)S

Diatomeas epilíticas (Bacillariophyceae) de los cursos de agua corriente del NO de la península ibérica (Galicia, España)

A catalog of Bacillariophyceae for the rivers of NW of Spain is made for the first time. It includes a re-examination of the taxa reported in previous publications, taxa cited during the last years of the rivers of the Galicia-Costa Hydrographic Demarcation, and a revision of the taxonomy, in line with the systematic and nomenclature changes, which have occurred mainly in recent years. The epilethic diatoms of the river basins of Galicia-Costa were sampled during the years 2005, 2006, and 2007, in May-June and September. The study was carried out in 41 localities distributed along 31 rivers, samples were taken in upstream and downstream sections. Diatom communities were compared in all upstream sections of these rivers draining from siliceous substrates. We identified 141 taxa of diatoms from the coast of Galicia. In this paper we present 15 new citations for Galicia, two for Spain and three for the Iberian Peninsula, in addition to a new species recently described. The dominant taxa are: Achnanthidium minutissimum, Achnanthes subhudsonis, Karayevia oblongella, Cocconeis placentula var. euglypta, Gomphonema rhombicum, and Navicula minima. Achnanthes subhudsonis was the most abundant species during the spring and summer months. The remaining species showed no relevant changes regardless of the time of year. The results indicate that the river diatoms of Galicia are an important component of the diversity of the ecosystemSe realiza por primera vez un catálogo de Bacillariophyceae para los ríos del NW de España. Se incluyen un nuevo examen de los táxones recogidos en publicaciones anteriores, datos de táxones citados durante los últimos años de los ríos de la demarcación hidrográfica de Galicia-Costa y una revisión de la taxonomía, en consonancia con los cambios sistemáticos y nomenclaturales, que se han producido sobre todo durante los últimos años. Se estudiaron las diatomeas epilíticas de las cuencas de los ríos de Galicia-Costa entre los años 2005, 2006 y 2007, durante dos temporadas diferentes: mayojunio y septiembre. El estudio se llevó a cabo en 41 localidades distribuidas a lo largo de 31 ríos, donde se tomaron muestras en tramos aguas arriba y aguas abajo. Las comunidades de diatomeas de estos ríos que drenan de sustratos silíceos fueron comparadas en todos los tramos de aguas arriba. Se identificaron 141 táxones de diatomeas de la costa de Galicia. En este trabajo presentamos 15 nuevas citas para Galicia, dos para España y tres para la Península Ibérica, además de una nueva especie recientemente descrita. Los táxones dominantes son: Achnanthidium minutissimum, Achnanthes subhudsonis, Karayevia oblongella, Cocconeis placentula var. euglypta, Gomphonema rhombicum, y Navicula minima. Achnanthes subhudsonis fue la especie más abundante durante los meses de primavera y verano. Las especies restantes no mostraron cambios pertinentes independientemente de la época del año. Los resultados indican que las diatomeas de los ríos de Galicia son un componente importante de la diversidad del ecosistemaThe financial support for this work has been provided by Augas de Galicia (Xunta de Galicia) through a contract with the University of Santiago de Compostela for the assessment of the stream water quality in rivers of Galicia-Costa using diatom metrics (2005—2007). We are indebted to Juan Manuel Antelo Cortizas (Department of Química-Física) and Teresa García Bernadal (researcher of Santiago de Compostela University) for their assistance during fieldwork and insightful comments on stream chemistry and ecologyS

Role of Exposure on the Microbial Consortiums on Historical Rural Granite Buildings

Local granite has been used throughout history in Galicia (NW Spain), forming the basis of much of the region’s architecture. Like any other rock, granite provides an ecological niche for a multitude of organisms that form biofilms that can affect the physical integrity of the stone. In this study, for the first time, characterization of the microbial consortium forming biofilms that developed on historical rural granite buildings is carried out using a combination of culture-dependent and next generation sequencing (NGS) techniques. Results pointed to differences in biofilm composition on the studied rural granite buildings and that of previously analyzed urban granite buildings, especially in terms of abundance of cyanobacteria and lichenized fungi. Exposure was corroborated as an important factor, controlling both the diversity and abundance of microorganisms on walls, with environmental factors associated with a northern orientation favoring a higher diversity of fungi and green algae, and environmental factors associated with the west orientation determining the abundance of lichenized fungi. The orientation also affected the distribution of green algae, with one of the two most abundant species, Trentepohlia cf. umbrina, colonizing north-facing walls, while the other, Desmococcus olivaceus, predominated on west-facing wallsThis study was partly financed through project CGL2016-79778-R (AEI/FEDER, UE) and Xunta de Galicia (ED431 2018/32). E. Fuentes was financially supported by a PhD fellowship contract, MICINN-FPI (BES-2017-079927)S

Automatic Pipeline for Detection and Classification of Phytoplankton Specimens in Digital Microscopy Images of Freshwater Samples

Presented at the 4th XoveTIC Conference, A Coruña, Spain, 7–8 October 2021.[Abstract] Phytoplankton blooming can compromise the quality of the water and its safety due to the negative effects of the toxins that some species produce. Therefore, the continuous monitoring of water sources is typically required. This task is commonly and routinely performed by specialists manually, which represents a major limitation in the quality and quantity of these studies. We present an accurate methodology to automate this task using multi-specimen images of phytoplankton which are acquired by regular microscopes. The presented fully automatic pipeline is capable of detecting and segmenting individual specimens using classic computer vision algorithms. Furthermore, the method can fuse sparse specimens and colonies when needed. Moreover, the system can differentiate genuine phytoplankton from other similar non-phytoplanktonic objects like zooplankton and detritus. These genuine phytoplankton specimens can also be classified in a target set of species, with special focus on the toxin-producing ones. The experiments demonstrate satisfactory and accurate results in each one of the different steps that compose this pipeline. Thus, this fully automatic system can aid the specialists in the routine analysis of water sources.This research was funded by Consellería de Cultura, Educación e Universidade, Xunta de Galicia through the predoctoral grant contract ref. ED481A 2021/147 and Grupos de Referencia Competitiva, grant ref. ED431C 2020/24; CITIC, Centro de Investigación de Galicia ref. ED431G 2019/01, receives financial support from Consellería de Educación, Universidade e Formación Profesional, Xunta de Galicia, through the ERDF (80%) and Secretaría Xeral de Universidades (20%).Xunta de Galicia; ED481A 2021/147Xunta de Galicia; ED431C 2020/24Xunta de Galicia; ED431G 2019/0

Fully automatic detection and classification of phytoplankton specimens in digital microscopy images

©2021. This manuscript version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/by-nc-nd/4.0/. This version of the article Rivas-Villar, D., Rouco, J., Carballeira, R., Penedo, M. G., & Novo, J. (2021). “Fully automatic detection and classification of phytoplankton specimens in digital microscopy images” has been accepted for publication in Computer Methods and Programs in Biomedicine, 200(105923), 105923. The Version of Record is available online at: https://doi.org/10.1016/j.cmpb.2020.105923.[Abstract]: Background and objective: The proliferation of toxin-producing phytoplankton species can compromise the quality of the water sources. This contamination is difficult to detect, and consequently to be neutralised, since normal water purification techniques are ineffective. Currently, the water analyses about phytoplankton are commonly performed by the specialists with manual routine analyses, which represents a major limitation. The adequate identification and classification of phytoplankton specimens requires intensive training and expertise. Additionally, the performed analysis involves a lengthy process that exhibits serious problems of reliability and repeatability as inter-expert agreement is not always reached. Considering all those factors, the automatization of these analyses is, therefore, highly desirable to reduce the workload of the specialists and facilitate the process. Methods: This manuscript proposes a novel fully automatic methodology to perform phytoplankton analyses in digital microscopy images of water samples taken with a regular light microscope. In particular, we propose a method capable of analysing multi-specimen images acquired using a simplified systematic protocol. In contrast with prior approaches, this enables its use without the necessity of an expert taxonomist operating the microscope. The system is able to detect and segment the different existing phytoplankton specimens, with high variability in terms of visual appearances, and to merge them into colonies and sparse specimens when necessary. Moreover, the system is capable of differentiating them from other similar objects like zooplankton, detritus or mineral particles, among others, and then classify the specimens into defined target species of interest using a machine learning-based approach. Results: The proposed system provided satisfactory and accurate results in every step. The detection step provided a FNR of 0.4%. Phytoplankton detection, that is, differentiating true phytoplankton from similar objects (zooplankton, minerals, etc.), provided a result of 84.07% of precision at 90% of recall. The target species classification, reported an overall accuracy of 87.50%. The recall levels for each species are, 81.82% for W. naegeliana, 57.15% for A. spiroides, 85.71% for D. sociale and 95% for the ”Other” group, a set of relevant toxic and interesting species widely spread over the samples. Conclusions: The proposed methodology provided accurate results in all the designed steps given the complexity of the problem, particularly in terms of specimen identification, phytoplankton differentiation as well as the classification of the defined target species. Therefore, this fully automatic system represents a robust and consistent tool to aid the specialists in the analysis of the quality of the water sources and potability.This work is supported by the European Regional Development Fund (ERDF) of the European Union and Xunta de Galicia through Centro de Investigación del Sistema Universitario de Galicia, ref. ED431G 2019/01.Xunta de Galicia; ED431G 2019/0