Techniques for designing drainage/subirrigation systems in the Lower Fraser Valley of British Columbia are examined in the present study. An attempt was made to formally define the overall goal in the design of such systems. Various difficulties were encountered in proceeding formally in the design. Therefore, a "branch and bound" approach was used in which a series of studies are conducted to focus our attention on the key issues of the problem and to regroup or eliminate other issues of secondary importance. A simple study showed that drainage designs seemed to be the limiting factors in drainage/subirrigation system designs for the Lower Fraser Valley. Therefore, subirrigation design was not considered in further analyses. The drainage requirements for different seasons were discussed. It was suggested that a drainage system designed to meet workability requirements in early spring should be more than sufficient to meet other seasonal requirements of interest from a drainage point of view. It was suggested that these requirements will be met by designing a drainage system that ensures at least one workable period of twelve days in March. A Markov chain model was proposed that can simulate the transitions in the water table elevations in response to weather. Design curves were presented for some local soils that can aid designers to perform drainage designs that satisfy requirements of the individual farmers. A study was undertaken to investigate the importance of uncertainty in soil parameters on the drainage system design. First and second order methods of analyzing uncertainty were applied to Hooghoudt's equation of designing drainage systems. The applicability of the uncertainty approach was extended to the numerical model of designing drainage systems based on the Boussinesq equation. An example problem was solved to illustrate how a drainage design criterion can be formulated when uncertainties due to both the climate and the soil parameters are present at the same time. Conclusions were drawn from the present study and recommendations were made for future work. The environmental impacts of agricultural drainage were discussed. They are included in the appendix because the main thrust of the thesis was on the design of drainage/subirrigation systems. Also, a design methodology was proposed in the appendix that can be used in designing drainage systems on a steady state basis in the absence of any knowledge about the saturated hydraulic conductivity of the soil or the location of the impermeable layer. / Graduate and Postdoctoral Studies / Graduate

Gymnotus pantherinus é uma espécie de peixe endêmica das drenagens costeiras brasileiras com distribuição desde o sul da Bahia até o Rio Grande do Sul, embora evidências morfológicas sugiram que esse táxon constitua um complexo de espécies. No presente trabalho, foram conduzidas análises filogenéticas com base em marcadores moleculares, mitocondriais e nucleares, com o objetivo de avaliar o status taxonômico do grupo. Padrões demográficos foram também inferidos para as populações de Gymnotus pantherinus (senso estrito). As análises filogenéticas sob o critério de Parcimônia, bem como as inferências bayesianas, mostraram que o grupo é composto por cinco linhagens geográficas estatisticamente bem suportadas. Das cinco linhagens identificadas, aquela composta por espécimes da Bahia e Espírito Santo é também suportada por evidências morfológicas, a qual propomos que seja reconhecida como uma nova espécie. As demais linhagens, das quais a mais recente é a de Gymnotus pantherinus senso estrito, foram consideradas como espécies incipientes. As análises populacionais revelaram que as populações de Gymnotus pantherinus (senso estrito) se apresentam altamente estruturadas, exibindo um alto índice de fixação e baixo compartilhamento de haplótipos, sendo reconhecidas três linhagens principais com alta associação geográfica. A maior diversidade genética foi encontrada na região do Vale do Ribeira e o clado SP/Sul é o que apresenta a divergência mais recente, a qual pode ter ocorrido após o Último Máximo Glacial. Populações localizadas a oeste da Serra do Mar (Paraíba do Sul, Alto Tietê e Alto Iguaçu) demonstram maior similaridade com drenagens adjacentes a leste, o que reforça a hipótese de captura de cabeceiras entre drenagens previamente postulada a partir do compartilhamento de fauna. Finalmente, os resultados apontam a existência de pelo menos cinco Unidades Evolutivas Significativas para a espécie, tendo implicações importantes na conservação dos riachos de Mata Atlântica. / Gymnotus pantherinus is an endemic fish species found in the Brazilian coastal drainages occurring from Bahia to Rio Grande do Sul states. Morphological evidence has suggested that Gymnotus pantherinus might constitute a species complex. In the present study, the taxonomic status of Gymnotus species group has been evaluated using both mitochondrial and nuclear markers. Demographic patterns have also been inferred for the Gymnotus pantherinus populations (stricto sensus). Parsimony and Bayesian phylogenetic inferences showed that the group is composed of five well supported geographic lineages. From those, a well supported lineage constituted by the specimens from Bahia and Espírito Santo states is also corroborated by morphological data. Thus, it is suggested that this lineage be recognized as a new species within Gymnotus. The other lineages, from which the most recent representative is the Gymnotus pantherinus lineage itself, have been considered as incipient species. The population analysis showed highly structured populations with low number of shared haplotypes and three main phylogenetic lineages with high geographic association. The higher genetic diversity was found in the Ribeira Valley region, while the clade SP/South was the most recently diverged, which may have occurred after the Last Glacial Maximum. Populations occurring west of the Serra do Mar were more closely related to the adjacent east drainages, which strengthens the hypothesis of headwaters stream capture. Finally, at least five evolutionary significant units can be recognized, with important implications for the conservation of Atlantic Forest streams.

O gênero Anchoviella Fowler, 1911 compreende 25 espécies de peixes de pequeno porte, de hábitos marinho, estuarino ou dulcícola, que ocorrem no continente americano. No Brasil foram registradas até o momento nove espécies do gênero, sendo seis de água doce. As espécies de água doce de Anchoviella foram descritas com base na análise de poucos exemplares e, em alguns casos em juvenis, certamente devido à escassez de material disponível nas coleções até o momento. Atualmente, o Museu de Zoologia da Universidade de São Paulo (MZUSP) e outras instituições brasileiras do gênero conseguiram reunir uma quantidade suficiente de material, tornando viável e oportuna a revisão taxonômica destas espécies. O presente estudo, portanto, teve como objetivos: i) redescrever as espécies de água doce do gênero Anchoviella presentes nas bacias Amazônica e do São Francisco; ii) definir com maior precisão a distribuição geográfica destas; iii) construir uma chave de identificação para o reconhecimento das espécies de Anchoviella presentes nas bacias Amazônica e do São Francisco. Foram encontradas oito espécies do gênero em estudo, cinco destas já descritas. São elas: Anchoviella alleni, A. carrikeri, A. guianensis, A. jamesi, A. vaillanti, A. sp.1, A. sp.2 e A. sp.3. A. nattereri fica no presente estudo como um nomen dubium. Tais espécies foram redescritas e comparadas quanto a caracteres morfológicos. Posteriormente, foi elaborada uma chave dicotômica incluindo além das sete espécies de Anchoviella encontradas no presente estudo, outras três espécies do gênero que habitam as áreas costeira e estuarina da região norte do Brasil. / The genus Anchoviella Fowler, 1911 includes 25 species of small fish with marine, estuarine or freshwater habits that are present in the Americas. In Brazil nine species of the genus were registered so far, six freshwater. The freshwater species of Anchoviella were described based on the analysis of a few specimens and, in some cases in juvenile specimens, certainly due to the scarcity of material available in collections so far. Currently, the Museu de Zoologia da Universidade de Sao Paulo (MZUSP) and other Brazilian institutions of this kind were able to gather a sufficient amount of material, becoming feasible and appropriate the taxonomic revision of these species. The present study therefore aimed to: i) redefine the freshwater species of the genus Anchoviella present in the Amazon and Sao Francisco River basin; ii) define more precisely the geographical distribution of these species; iii) construct an identification key for the recognition of species Anchoviella present in the Amazon and Sao Francisco basin. We have found eight species of the genus in the study, five of these already described. They are: A. alleni, A. carrikeri, A. guianensis, A. jamesi, A. vaillanti, A. sp.1, A. sp.2 and A. sp.3. A. nattereri is in this study as a nomen dubium. These species were redescribed and compared based on morphological characters. It was later developed a dichotomous key that include besides the seven species Anchoviella found in this study, three other species of which inhabit the coastal and estuarine areas of northern Brazil.

The anthropic action has changed the water quality of rivers and its tributaries as well as the sheets. In rural areas, where there is the predominance of familiar agriculture linked to the agroindustry, this problem is generalized. This work has the objectives of (a) to monitor the quality of superficial waters of the main stream in a head hydrographic microbasin, (b) to evaluate the quality of the human consumption water and (c) to evaluate the efficiency of two stations of drainages treatment through the roots zones. In order to do this, samples of four points of the main stream and five spring waters used to the human consumption placed in the hydrographic microbasin of Arroio Lino, Agudo, RS, were done. Besides that, samples of effluents in the entry and in the exit of two stations of drainages treatment were gathered. The amount of N-ammonia, N-nitrate, P-total, P-soluble, total fecal microorganisms and Escherichia coli were analyzed. In these stations of drainages treatment, besides the microbiological physical-chemical parameters, the indicators of organic material (biochemical and chemical demand of oxygen) were also analyzed. The Arroio Lino s water always has been contaminated with total fecal microorganisms and they overtake the limits established by CONAMA to classes 2 waters. At the same time, the spring waters always have presented microbiological contamination, mainly by total fecal microorganisms, exceeding the maximum values allowed by the Health Ministry. The spring waters that have not suffered technical intervention are the ones that have presented the major problems, that is, it is obvious that the construction of springs upon supervision enables to decrease the contamination. The stations of drainages treatment are extremely efficient in the values reduction of the physical-chemical and microbiological parameters as well as in the indication of effluent organic material, however for many times they do not fit to the limits established by CONSEMA. / A ação antrópica tem alterado a qualidade da água de rios e seus afluentes e, inclusive, do lençol freático. Nas áreas rurais com predomínio de agricultura familiar integrada à agroindústria este problema é generalizado. Este trabalho tem como objetivos (a) monitorar a qualidade das águas superficiais do arroio principal numa microbacia hidrográfica de cabeceira, (b) avaliar a qualidade da água de consumo humano, e (c) avaliar a eficiência de duas estações de tratamento de esgotos por meio de zona de raízes. Para isso, foram realizadas amostragens de quatro pontos do arroio principal e cinco fontes de água utilizadas para o consumo humano, localizados na microbacia hidrográfica do Arroio Lino, Agudo - RS. Além disso, coletaram-se amostras de efluentes na entrada e na saída de duas estações de tratamento de esgotos. Analisaram-se os teores de N-amônia, N-nitrato, P-total e P-solúvel; coliformes totais e Escherichia coli. Para as estações de tratamento de esgotos além dos parâmetros físico-químicos e microbiológicos foram analisados os indicadores de matéria orgânica (demanda bioquímica de oxigênio e demanda química de oxigênio). Os resultados mostraram que, durante o período avaliado, a água do Arroio Lino sempre esteve contaminada com coliformes totais e ultrapassam os limites estabelecidos pelo CONAMA para águas classe 2. Ao mesmo tempo, a água das fontes sempre apresentou contaminação microbiológica, principalmente por coliformes totais, excedendo os valores máximos permitido pelo Ministério da Saúde. As fontes que não sofreram intervenção técnica foram as que apresentam maiores problemas, ficando evidente que a construção de fontes sob orientação permite diminuir a contaminação. As estações de tratamento de esgotos foram eficientes na diminuição dos valores dos parâmetros físicoquímicos, microbiológicos e de indicação de matéria orgânica dos efluentes, porém, em muitas ocasiões não se enquadraram nos limites estabelecidos pelo CONSEMA.

O gênero Anchoviella Fowler, 1911 compreende 25 espécies de peixes de pequeno porte, de hábitos marinho, estuarino ou dulcícola, que ocorrem no continente americano. No Brasil foram registradas até o momento nove espécies do gênero, sendo seis de água doce. As espécies de água doce de Anchoviella foram descritas com base na análise de poucos exemplares e, em alguns casos em juvenis, certamente devido à escassez de material disponível nas coleções até o momento. Atualmente, o Museu de Zoologia da Universidade de São Paulo (MZUSP) e outras instituições brasileiras do gênero conseguiram reunir uma quantidade suficiente de material, tornando viável e oportuna a revisão taxonômica destas espécies. O presente estudo, portanto, teve como objetivos: i) redescrever as espécies de água doce do gênero Anchoviella presentes nas bacias Amazônica e do São Francisco; ii) definir com maior precisão a distribuição geográfica destas; iii) construir uma chave de identificação para o reconhecimento das espécies de Anchoviella presentes nas bacias Amazônica e do São Francisco. Foram encontradas oito espécies do gênero em estudo, cinco destas já descritas. São elas: Anchoviella alleni, A. carrikeri, A. guianensis, A. jamesi, A. vaillanti, A. sp.1, A. sp.2 e A. sp.3. A. nattereri fica no presente estudo como um nomen dubium. Tais espécies foram redescritas e comparadas quanto a caracteres morfológicos. Posteriormente, foi elaborada uma chave dicotômica incluindo além das sete espécies de Anchoviella encontradas no presente estudo, outras três espécies do gênero que habitam as áreas costeira e estuarina da região norte do Brasil. / The genus Anchoviella Fowler, 1911 includes 25 species of small fish with marine, estuarine or freshwater habits that are present in the Americas. In Brazil nine species of the genus were registered so far, six freshwater. The freshwater species of Anchoviella were described based on the analysis of a few specimens and, in some cases in juvenile specimens, certainly due to the scarcity of material available in collections so far. Currently, the Museu de Zoologia da Universidade de Sao Paulo (MZUSP) and other Brazilian institutions of this kind were able to gather a sufficient amount of material, becoming feasible and appropriate the taxonomic revision of these species. The present study therefore aimed to: i) redefine the freshwater species of the genus Anchoviella present in the Amazon and Sao Francisco River basin; ii) define more precisely the geographical distribution of these species; iii) construct an identification key for the recognition of species Anchoviella present in the Amazon and Sao Francisco basin. We have found eight species of the genus in the study, five of these already described. They are: A. alleni, A. carrikeri, A. guianensis, A. jamesi, A. vaillanti, A. sp.1, A. sp.2 and A. sp.3. A. nattereri is in this study as a nomen dubium. These species were redescribed and compared based on morphological characters. It was later developed a dichotomous key that include besides the seven species Anchoviella found in this study, three other species of which inhabit the coastal and estuarine areas of northern Brazil.

Les liens entre la diversité et l'adaptation des populations bactériennes à leur environnement constituent une problématique importante en écologie microbienne. L'accès à de nombreux génomes permet aujourd'hui des avancées intéressantes dans ce domaine. Plusieurs souches du genre Thiomonas et appartenant à la même espèce, Tm. arsenitoxydans 3As et Tm. spp. CB1, CB2, CB3 et CB6, ont été isolées d'un drainage minier acide (DMA) à Carnoulès (Gard). La comparaison de leur génome a permis d'affiner leur phylogénie et de mettre au jour des différences de contenu génétique liées à des îlots génomiques. Certaines de ces différences ont été corrélées expérimentalement avec des différences fonctionnelles concernant l'oxydation de l'arsénite (As(III)), la dégradation de l'urée et la biosynthèse de biofilm, et confèrent potentiellement un avantage sur le site (meilleure résistance à l'As(III), précipitation des métaux et augmentation du pH, protection des cellules). La comparaison de la synténie des génomes de Tm. arsenitoxydans 3As avec Tm. sp CB2 et Tm. intermedia K12 (non isolée de ce DMA) a montré que le génome de Tm. sp. CB2 a subi plusieurs remaniements importants. Ces types de réarrangements pourraient être en partie à l'origine de l'apparition de variants "super-résistants" à l'As(III) dans la population. En particulier, plusieurs copies d'un élément intégratif et conjugatif portant l'opéron aioBA codant l'arsénite oxydase ont été détectées chez deux variants, ce qui pourrait en partie expliquer leur résistance accrue à l'As(III). La proportion de variants est plus importante en présence d'As(III) au sein des biofilms, et des données de transcriptomique ont en effet montré que ces remaniements seraient en partie causés par des systèmes de réparation de l'ADN suite à des dommages liés au stress oxydant induit par l'As(III). Le développement en biofilm et la présence d'As(III) modulerait donc la flexibilité génomique et le potentiel adaptatif de Tm. sp. CB2. Ces données suggèrent que cette souche, avec Tm. sp. CB3, possèdent un génome visiblement plus flexible que les autres. Les souches Tm. arsenitoxydans 3As et Tm. spp. CB1 et CB6, contrairement à Tm. spp. CB2 et CB3, forment un groupe distinct d'un point de vue phylogénétique et fonctionnel ("groupe 3As"), suggérant qu'elles occupent une niche écologique spécifique et pourraient constituer un écotype. La population de Thiomonas de ce DMA serait donc composée d'au moins un écotype stable et de souches au génome plus instable, dont le potentiel adaptatif plus important serait influencé par l'As(III) et le développement en biofilm. / Understanding the link between diversity and adaptation in natural bacterial populations represents an important issue in microbial ecology. The amount of whole genome sequencing data currently available has allowed for interesting advances in this field. Several strains from the genus Thiomonas belonging to the species, Tm. arsenitoxydans (3As) and Tm. spp. (CB1, CB2, CB3 and CB6), were isolated from the acid mine drainage (AMD) at Carnoulès (Gard, France). Comparison among genomes allowed for a better definition of their phylogenetic relationships and highlighted differences in genetic content, which is essentially due to the presence of genomic islands. Some of these differences were experimentally correlated with functional traits concerning arsenite oxidation, urea degradation, and biofilm biosynthesis, and are potentially beneficial in situ (leading to an enhanced resistance to arsenite (As(III)), metal precipitation, and an increase in pH, ultimately protecting cells). The comparison of genome synteny of Tm. arsenitoxydans 3As, Tm. sp CB2, and Tm. intermedia K12 (not isolated from this AMD) show several important genomic rearrangements exist in Tm. sp CB2. This type of rearrangements could be involved in the emergence of arsenite "super-resistant" variants in the Tm. sp CB2 population. In particular, several copies of an integrative and conjugative element (ICE) containing the aioBA operon coding arsenite oxidase were detected in the genomes of two variants, which could explain their higher levels of resistance to As(III). The percentage of variants in biofilm culture is higher when grown in the presence of As(III), and transcriptomic data suggests that genomic rearrangements probably occurred through DNA repair systems following damage caused by As(III) induced oxidative stress. Therefore, biofilm development and As(III) appear to allow for the adaptation of Tm. sp. CB2 genome flexibility and evolutionary potential. These data suggest that CB2 and Tm. sp. CB3 have more flexible genomes than the other strains. Tm. arsenitoxydans 3As and Tm. spp. CB1 and CB6 form both a phylogenetic and functional cluster ("3As group") suggesting that they occupy a specific ecological niche and therefore could represent an ecotype of the genus Thiomonas. The Thiomonas population from the Carnoulès AMD might therefore consist of at least one stable ecotype as well as other strains with more instable genomes, whose higher adaptive potential could be affected by As(III) and biofilm development.

Gymnotus pantherinus é uma espécie de peixe endêmica das drenagens costeiras brasileiras com distribuição desde o sul da Bahia até o Rio Grande do Sul, embora evidências morfológicas sugiram que esse táxon constitua um complexo de espécies. No presente trabalho, foram conduzidas análises filogenéticas com base em marcadores moleculares, mitocondriais e nucleares, com o objetivo de avaliar o status taxonômico do grupo. Padrões demográficos foram também inferidos para as populações de Gymnotus pantherinus (senso estrito). As análises filogenéticas sob o critério de Parcimônia, bem como as inferências bayesianas, mostraram que o grupo é composto por cinco linhagens geográficas estatisticamente bem suportadas. Das cinco linhagens identificadas, aquela composta por espécimes da Bahia e Espírito Santo é também suportada por evidências morfológicas, a qual propomos que seja reconhecida como uma nova espécie. As demais linhagens, das quais a mais recente é a de Gymnotus pantherinus senso estrito, foram consideradas como espécies incipientes. As análises populacionais revelaram que as populações de Gymnotus pantherinus (senso estrito) se apresentam altamente estruturadas, exibindo um alto índice de fixação e baixo compartilhamento de haplótipos, sendo reconhecidas três linhagens principais com alta associação geográfica. A maior diversidade genética foi encontrada na região do Vale do Ribeira e o clado SP/Sul é o que apresenta a divergência mais recente, a qual pode ter ocorrido após o Último Máximo Glacial. Populações localizadas a oeste da Serra do Mar (Paraíba do Sul, Alto Tietê e Alto Iguaçu) demonstram maior similaridade com drenagens adjacentes a leste, o que reforça a hipótese de captura de cabeceiras entre drenagens previamente postulada a partir do compartilhamento de fauna. Finalmente, os resultados apontam a existência de pelo menos cinco Unidades Evolutivas Significativas para a espécie, tendo implicações importantes na conservação dos riachos de Mata Atlântica. / Gymnotus pantherinus is an endemic fish species found in the Brazilian coastal drainages occurring from Bahia to Rio Grande do Sul states. Morphological evidence has suggested that Gymnotus pantherinus might constitute a species complex. In the present study, the taxonomic status of Gymnotus species group has been evaluated using both mitochondrial and nuclear markers. Demographic patterns have also been inferred for the Gymnotus pantherinus populations (stricto sensus). Parsimony and Bayesian phylogenetic inferences showed that the group is composed of five well supported geographic lineages. From those, a well supported lineage constituted by the specimens from Bahia and Espírito Santo states is also corroborated by morphological data. Thus, it is suggested that this lineage be recognized as a new species within Gymnotus. The other lineages, from which the most recent representative is the Gymnotus pantherinus lineage itself, have been considered as incipient species. The population analysis showed highly structured populations with low number of shared haplotypes and three main phylogenetic lineages with high geographic association. The higher genetic diversity was found in the Ribeira Valley region, while the clade SP/South was the most recently diverged, which may have occurred after the Last Glacial Maximum. Populations occurring west of the Serra do Mar were more closely related to the adjacent east drainages, which strengthens the hypothesis of headwaters stream capture. Finally, at least five evolutionary significant units can be recognized, with important implications for the conservation of Atlantic Forest streams.

L'ancienne mine de plomb et de zinc de Carnoulès (Gard, France) a généré 1.5 Mt de déchets d'où émerge un drainage de mine aux eaux acides alimentant un ruisseau, le Reigous. Ce site fournit un exceptionnel exemple d'adaptation à un environnement extrême en raison des eaux acides (pH~3) et de très fortes concentrations en métaux et métalloïdes, particulièrement en As. Dans les 30 premiers mètres du ruisseau, l'activité bactérienne conduit à un phénomène de remédiation naturelle avec la co-précipitation de 20 à 60% de l'As dissous avec du fer. Les bactéries présentes dans les sédiments du ruisseau ont dans un premier temps été décrites par clonage/séquençage du gène de l'ARNr 16S, puis les membres actifs des communautés bactériennes ont été révélés par une approche de métaprotéomique. L'étude des Archaea au sein des sédiments a révélé la présence de groupes impliqués dans la méthanogénèse ou dans l'oxydation de l'ammoniac qui pourraient participer au cycle du carbone ou de l'azote. Les eucaryotes ont été caractérisés pour la première fois sur ce site par pyroséquençage, mettant en évidence une forte proportion de champignons (60%). Enfin, l'étude des variations spatiotemporelles des populations bactériennes dans les eaux a conduit à l'identification de 6801 OTUs dont des phyla encore jamais identifiés sur ce site. La concentration en arsenic, la température et le potentiel redox semblent jouer un rôle dans la structuration de ces communautés. Ce travail de thèse a ainsi contribué à une meilleure connaissance des microorganismes présents (Bactéries, Archaea, Eucaryotes) et de leurs dynamiques spatiotemporelles en relation avec les paramètres physicochimiques du milieu. / Acidic mining drainage generated at Carnoulès, a former Pb-Zn mine (Gard, France) coincides with the spring of the Reigous Creek. This site provides an exceptional example of adaptation to extreme environments due to its acidic water (pH~3) and very high concentrations of metals and metalloids, particularly arsenic. During the first 30 m of downflow in Reigous Creek, natural remediation occurred, with co-precipitation of 20 to 60% of the dissolved arsenic with iron, mediated by bacteria. Bacterial communities inhabiting the creek sediments were first described by cloning/sequencing of the 16S rRNA genes and the active members were identified by a metaproteomic approach. A survey of the archaeal community in the sediment highlighted the presence of sequences phylogenetically related to methanogenic Archaea and to ammonia oxidizers, which could be involved in carbon and nitrogen biochemical cycling. The Eukaryotic communities were studied for the first time at this site by pyrosequencing, revealing that around 60% of the sequences belonged to Fungi. Finally, the study of the spatiotemporal variations of the water bacterial communities allowed the identification of 6801 OTUs including sequences of taxa never detected before. The environmental variables significantly correlated with bacterial community dynamics appear to be arsenic concentration, temperature and Eh. This PhD work has contributed to a better understanding of the spatiotemporal dynamics of microorganisms (Bacteria, Archaea, Eukaryotes) in relation with the physicochemical parameters of their environment.