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The composition of gut microbes affects host weight, immune function, and disease status, and is sensitive to diet, environment, and pharmaceutical exposure. The gut microbiome modulates the toxicity and bioavailability of chemical stressors, however the effects of chemicals on the gut microbiome of aquatic biota are largely unknown. The Waterloo and Kitchener wastewater treatment plants (WWTPs) release effluents containing antibiotics, pharmaceuticals, and other contaminants into the Grand River (ON) that may negatively affect the gut microbiome of downstream organisms. In this study done in Fall 2018, I collected freshwater mussels (Lasmigona costata), several species of insect larvae, and riparian spiders (Tetragnathidae) from sites upstream and downstream of these WWTPs. The gut microbiome was analyzed following the extraction, PCR amplification, and sequencing of bacterial DNA using the V3-V4 hypervariable regions of the 16S rRNA genetic barcode. Changes in the relative abundance of major gut microbiome phyla were observed in all targeted aquatic organisms downstream of WWTPs except Hydropsychidae. Shannon alpha diversity, a measure of bacterial abundance and evenness, differed significantly among sites for mussels (one-way ANOVA: F=7.894, p=0.001), spiders (F=4.788, p=0.01), Perlidae (F=3.1, p=0.0056), Hydropsychidae (F=3.674, p=0.0014), and Heptageniidae (F=2.715, p=0.0143), but not for Baetidae and Ephemerellidae. In sites downstream of the Waterloo WWTP, alpha diversity decreased in spiders, while in sites downstream of the Kitchener WWTP diversity decreased in mussels and Perlidae, while increasing for spiders. Bray-Curtis beta diversity, a measure of dissimilarity between bacterial communities, was significantly dissimilar among sites in all invertebrate taxa (Permanova: p<0.02). Upstream sites differed from downstream Waterloo sites in spiders, Perlidae, and Hydropsychidae (Adonis pairwise: p<0.05), while upstream mussels, spiders, Perlidae, and Hydropsychidae differed from downstream Kitchener sites (p<0.05). Additionally, effluent-derived bacteria were found in the microbiomes of aquatic invertebrates downstream of the WWTPs and not upstream. Taxa was also a significant driver of bacterial composition and diversity in invertebrates. These results indicate that the gut microbiome of downstream organisms differed from the bacterial composition observed in the same invertebrate taxa upstream of the WWTPs, potentially leading to altered host health. This adds to our understanding of how chemical stressors impact the gut microbiome of aquatic and riparian biota; however, future studies are needed to investigate linkages between the gut microbiome and health of these species. / Thesis / Master of Science (MSc)

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.

Les milieux aquatiques en zone urbaine sont reconnus comme des îlots de biodiversité qui offrent de nombreux services écologiques. Dans cette étude, nous avons utilisé les macroinvertébrés comme bioindicateurs de la qualité écologique des étangs, petits lacs et marais de l’Île de Montréal. Les macroinvertébrés ont été récoltés durant l’été 2011 dans la zone littorale de 20 sites variant par leur urbanisation et leurs caractéristiques limnologiques. Nous avons évalué la variation dans la richesse en taxa, les indices de diversité et plusieurs métriques basées sur la composition taxonomique ou les traits fonctionnels. Nous avons déterminé la réponse des métriques aux changements dans l’urbanisation, l’aménagement et les conditions des plans d’eau. Notre étude montre que les étangs, marécages et petits lacs constituent des réserves importantes de biodiversité en zone urbaine. Les marécages naturels et les étangs et lacs permaments avaient une meilleure qualité écologique et supportaient des communautés de macroinvertébrés plus diverses et abondantes que les petits étangs temporaires aménagés. Le couvert de végétation aquatique, l’enrichissement en nutriments et en matière organique ainsi que la biomasse des algues expliquaient le plus de variation dans les macroinvertébrés. Les aménagements, la densité urbaine et la permanence de l’eau avaient aussi une bonne influence. Les métriques univariées avaient moins de potentiel que les métriques multivariées. Nous avons discuté les implications de notre étude pour le suivi environnemental de la biodiversité et la qualité écologique des milieux aquatiques en zone urbaine. / Aquatic ecosystems in urban landscapes are now recognized as good islets of biodiversity and valuable environments providing ecological services. However, more knowledge is needed to assess their ecological quality. Benthic macroinvertebrates are widely used as bioindicators, but rarely for urban ecosystems. In this study, we used macroinvertebrates to evaluate the ecological quality of urban ponds and lakes in the island of Montreal. We collected macroinvertebrates during summer 2011 in the littoral zone of 20 waterbodies varying in urban and limnological characteristics. We evaluated spatio-temporal variation in several diversity and biotic indices and multiple metrics based on taxonomic composition and functional traits. We investigated if macroinvertebrate metrics responded to variation in urban land-use, pond management and limnological conditions. Our study showed that small waterbodies, as ponds, lakes and marshes are important resources for sustaining aquatic biodiversity in urban landscapes. Natural wetlands and artifical permanent ponds had higher ecological quality and supported more diverse and abundant macroinvertebrates than artificial managed temporary ponds in municipal parks. Vegetation cover, nutrient and organic contents, and algal biomass were the most important factors explaining spatial variation in macroinvertebrate metrics. Pond management, urban density, and water permanence were also influencial factors. Univariate metrics had less potential than multivariable metrics to assess the responses of macroinvertebrates to environmental features. We discussed the implications of our study for management and quality assessment of urban ponds.

Shore zones of large rivers are hot spots of biodiversity and contribute significantly to riverine ecosystem functioning. Today, shore degradation and other structural impair-ments like river straightening and channelization are strong impact factors on river ecosystem health. However, we still lack a thorough understanding of how structural shore zone degradation affects benthic community composition and their inherent ecosystem functions. In this thesis I tested the influence of training structure induced environmental factors on benthic macroinvertebrate community composition and the share of non-native species. Moreover, I assessed the community-associated ecosystem functions in terms of secondary production and resource utilization. In the main channel, communities were composed of only a few specialized taxa with low abundances, which contributed little to riverine secondary production. This is probably due to the harsh conditions produced by constantly high flow velocities and relocation of the fine sandy sediment. Main channel habitats were hardly affected by the adjacent training structure. Hence, species compositions and productivities were similar at all investigated main channel sites. By contrast, each of the shore communities was diverse, highly abundant and productive in comparison to the main channel. However, variations between shore structure communities and their ecosystem functions were prominent. One particular training structure, i.e. the off-bankline revetment, bore the most diverse and by far most productive benthic community, which utilized vast total amounts of basal resources (1,323 g DM m-² y-1). Varying sediment compositions, availability of macrophytes and diverse flow velocities, including lentic conditions, were revealed as key factors for increasing biodiversity, secondary production and resource utilization. Allochthonous boulder habitats were generally highly prone to non-native species invasion. Neozoa proved less productive than many native community members and consumed minor relative and total amounts of the prevailing resource pelagic algae. The present quantitative comparison of shore type specific effects on biodiversity, biomass and productivity provides managers with a tool to improve the ecological attributes of large river ecosystems with an unchangeable, impaired macrostructure. In its entirety, this thesis constitutes a sound basis to increase the mechanistic understanding of the way in which shore zone manipulation can affect riverine benthic communities and their associated ecosystem functions. / Die Uferbereiche großer Flüsse sind für die Biodiversität und Funktion dieser Ökosys-teme von enormer Bedeutung. Uferdegradierung und Kanalisierung gehören zu wichti-gen Faktoren, die Flussökosysteme nachhaltig beeinträchtigen. Wie sich anthropogene Umstrukturierungen der Uferbereiche auf die Zusammensetzung benthischer Ge-meinschaften und deren Ökosystemfunktion auswirken ist jedoch weitestgehend unbe-kannt. In dieser Arbeit werden die Effekte von uferspezifischen Habitatfaktoren auf die Komposition des Makrozoobenthos und den Anteil an Neozoen getestet. Zudem wurden die gemeinschaftsassoziierten Ökosystemfunktionen in Bezug auf Sekundärproduktion und Ressourcennutzung erfasst und bewertet. Die benthische Gemeinschaft des Hauptstroms bestand lediglich aus wenigen spezialisierten Arten, welche nur geringfügig zur Gesamtsekundärproduktion des Flusses beitrugen. Dies war vermutlich auf die rauen Bedingungen im Hauptstrom (insbesondere hohe Strömungsgeschwindigkeiten und damit verbundener Sedimenttransport) zurückzuführen. Die Makrozoobenthosgemeinschaften des Hauptroms wurden von den jeweils angrenzenden Ufertypen nicht beeinflusst. Im Gegensatz zum Hauptstrom zeigte jeder der untersuchten Ufertypen hohe Dichten an benthischen Invertebraten wobei sich Zusammensetzung und Funktion der Artengemeinschaften zwischen den Ufertypen stark unterschieden. Dabei brachte das Parallelwerk die diverseste und produktivste Makroinvertebratenfauna hervor, welche enorme Mengen basaler Ressourcen ingestierte (1,323 g DM m-2y-1). Hauptfaktoren für eine Erhöhung von Biodiversität, Sekundärproduktion und Ressourcennutzung waren neben variablen Sedimentzusammensetzungen und Makrophytenbeständen sich oft ändernde Fließgeschwindigkeiten mit lentischen Phasen. Allochthone Steinhabitate waren generell anfällig für die Invasion nicht heimischer Arten. Diese Neozoen waren weniger produktiv als viele heimische Taxa und nutzten nur geringe Mengen pelagischer Algen, welche die meist verfügbare Ressource darstellten. Aus dem ökologischen Vergleich der verschiedenen Ufertypen lassen sich Managementempfehlungen zur Verbesserung des ökologischen Zustandes in Bezug auf Biodiversität und Ökosystemfunktionen ableiten, welche für große Flüsse mit degradierter und unveränderbarer Makrostruktur in Betracht gezogen werden können. In ihrer Gesamtheit liefert diese Arbeit ein fundiertes mechanistisches Verständnis über die Effekte von Ufermanipulationen auf benthische Gemeinschaften und deren assoziierte Ökosystemfunktionen in großen Flüssen.

O presente estudo teve como objetivo avaliar a qualidade ambiental do reservatório de Salto Grande (Americana, SP), localizado em área de intensa urbanização e atividade industrial. Utilizou-se, para tanto, análises físicas e químicas na água e no sedimento, bioensaios de toxicidade e estrutura (composição e densidade) da fauna de macroinvertebrados bentônicos em quatro períodos (Maio, Agosto, Novembro de 2000 e Fevereiro de 2001). Pela análise de nutrientes na água constatou-se que as concentrações são elevadas, principalmente do íon amônio e do fosfato total, os quais estiveram acima do limite estabelecido pela resolução CONAMA 20/86 e, com base no Índice do Estado Trófico o sistema caracteriza-se como eutrófico ou hipereutrófico, dependendo do período e da localização das estações amostradas, verificando-se a redução na concentração de nutrientes e conseqüentemente, do estado trófico, no sentido do rio para a barragem. A concentração de nutrientes no sedimento também foi elevada quando comparada a outros reservatórios e a análise granulométrica demonstra que as estações centrais do reservatório possuem sedimento silte-argiloso enquanto as estações marginais e o rio Atibaia apresentam sedimentos arenosos. A análise de metais indica que a água e o sedimento do sistema encontram-se contaminados para todos os metais estudados (Cd, Cu, Cr, Fe, Mg e Mn), exceto para Zn na água e Pb no sedimento. A análise de metais nos organismos bentônicos aponta para uma bioacumulação de Cd, Cu, Fe, Mg, Mn, e Zn o mesmo não sendo observado para Pb e Cr. Nos bioensaios de toxicidade aguda verificou-se, para Chironomus xanthus, maior toxicidade no rio Atibaia, com 61% de mortalidade em Novembro/2000, enquanto que para Daphnia similis a toxicidade máxima (100% de imobilidade em Agosto/2000) foi registrada nas estações próximas à barragem. A análise da fauna de macroinvertebrados bentônicos demonstra a predominância, nas estações centrais do reservatório (mais profundas), de organismos pertencentes à Classe Oligochaeta e nas estações marginais (zona litorânea) a fauna é mais diversa, sendo composta pela Classe Oligochaeta, Filo Mollusca e Ordem Ephemeroptera (Classe Insecta). A fauna do rio Atibaia é formada, predominantemente, pelas Classes Hirudinea e Oligochaeta. O estágio avançado da eutrofização do reservatório fez com que a fauna de macroinvertebrados fosse reduzida, quando comparada à estudos anteriores, possivelmente devido ao desencadeamento de processos associados ao grande aporte de nutrientes, como a redução na concentração de oxigênio dissolvido ou devido ao aporte contínuo de diversos metais para o sistema e, provavelmente, esteja havendo uma processo de substituição de espécies por organismos da Classe Oligochaeta, como a Família Tubificidae, que são mais tolerantes aos diversos tipos de poluição. Conclui-se que as altas concentrações de nutrientes e metais, com valores fora dos padrões estabelecidos pelos órgãos ambientais, na água e no sedimento do reservatório, relacionam-se com as atividades desenvolvidas na bacia hidrográfica, e indicam os impactos decorrentes desta utilização e seu reflexo nas características físicas, químicas, toxicológicas e biológicas do sistema. / The goal of this work was to asses the environmental quality of Salto Grande reservoir (Americana, SP), located in an urban area with high industrial activities. Physical and chemical analyses were made in water and sediment, toxicity bioassays and structure (composition and density) of benthic organisms in four months (May, August, November 2000 and February 2001). The water nutrients analyses demonstrated high concentrations, mainly of ammonia ion and total phosphate, exceeding the limits from CONAMA 20/86, and based on the Trophic State Index, the reservoir was classified as eutrophic or hipereutrophic, depending on the months and the sampling stations, verified by a reduction on nutrients concentrations and in the trophic state, in the river-dam direction. The nutrients concentrations in the sediment was also elevated when compared with others reservoirs and the grain size composition demonstrated that the central sampling stations had silt-clay composition while the shore sampling stations and the Atibaia river had sand composition. The metals analysis indicates that water and sediment were contaminated by Cd, Cu, Cr, Fe, Mg, e Mn, with exception for Zn in the water and Pb in the sediment. The metals analysis in the benthic organisms indicates a bioaccumulation of Cd, Cu, Fe, Mg, Mn and Zn, with exception for Pb and Cr. The acute toxicity bioassays verified, for Chironomus xanthus, higher toxicity in the Atibaia river, with 61% of mortality in November 2000, while for Daphnia similis the maximum toxicity (100% of immobility in August 2000) was observed on the sampling stations near the dam. The analysis of benthic organisms demonstrates the predominance of Oligochaeta, on central sampling stations (with higher profundity), and a higher diversity fauna, mainly by Oligochaeta, Mollusca and Ephemeroptera (Insecta), on the shore sampling stations. The Atibaia river fauna is composed mainly by Hirudinea and Oligochaeta. The higher eutrophication process in the reservoir probably was the cause of the reduction of macroinvertebrates fauna, when compared with studies in the past. The major process of these problems are the elevated input of nutrients, reduction on the dissolved oxygen and the input of metals, resulting in the substitution of the species for Oligochaeta organisms (Tubificidae), which are tolerant to different pollutants. To conclude, the high concentrations in the water and sediment for nutrients and metals, with values that exceed the limits from Environmental Agency, were related to the activities developed in the Watershed, indicating impacts produced by this utilization and its effects on the physical, chemical toxicological and biological characteristics of the system.

Os macroinvertebrados bentônicos são importantes componentes nos ecossistemas aquáticos devido à sua participação no fluxo de energia e na ciclagem de nutrientes, recebendo gradativamente maior atenção nos estudos ecológicos nas últimas décadas. O presente estudo visa uma caracterização limnológica comparativa de quatro lagoas do sistema de lagos do Vale do Rio Doce, MG (lagoas Águas Claras, Almécega, Verde e Carioca), e o estudo dos macroinvertebrados bentônicos, com ênfase na composição taxonômica, distribuição espaçotemporal e diversidade, além de uma avaliação de possíveis relações com a ocorrência de espécies exóticas neste sistema. As lagoas encontram-se na depressão interplanáltica do Vale do Rio Doce, formada por uma rica rede de drenagem, circundada por remanescentes de Mata Atlântica (19 'GRAUS' 45’ 25,7" e 19 'GRAUS' 53’ 11,6" S; 42 'GRAUS' 37’ 35,6" e 42 'GRAUS' 35’ 11,3" W). Amostragens para análises físicas, químicas e biológicas foram realizadas em setembro e dezembro de 2002 e março e junho de 2003. As amostragens de sedimento para análises de composição granulométrica e da comunidade de macroinvertebrados bentônicos foram realizadas com draga do tipo Van Veen (337 'CM POT.2'), em um total de 77 estações de coleta e em quatro períodos de amostragem. Foram identificados 56 táxons, sendo 2 pertencentes ao Filo Mollusca, 13 à Classe Oligochaeta, 1 à Classe Hirudinae, 1 ao Filo Nematoda e 41 à Classe Insecta. Desses últimos, 27 pertencem à família Chironomidae. A maior riqueza de táxons foi registrada na lagoa Carioca (43 táxons) e a menor na lagoa Águas Claras (27 táxons). Melanoides tuberculata, um molusco invasor, foi o táxon numericamente dominante nas lagoas Águas Claras e Almécega. Na lagoa Verde esse molusco ocorreu em densidade média 5 vezes menor do que nas lagoas anteriormente citadas onde suas populações já se encontram bem estabelecidas. Na lagoa Carioca não há ocorrência desse molusco, e nesta lagoa foi registrada a maior riqueza de táxons entre as lagoas estudadas, sendo os Chironomidae os macroinvertebrados bentônicos mais representativos. Sazonalmente ocorreram diferenças na densidade das populações. Existem também diferenças quanto à composição taxonômica da comunidade bentônica entre as regiões litorânea e limnética, evidenciando a compartimentalização do sistema. Os sedimentos das lagoas Águas Claras, Almécega e Verde tem baixo conteúdo de matéria orgânica, sendo do tipo mineral e arenoso, enquanto o da lagoa Carioca é do tipo barrento e orgânico. Em relação às variáveis limnológicas, o pH é ligeiramente ácido e as águas bem oxigenadas. As concentrações de nutrientes na coluna d’água são relativamente baixas podendo as lagoas Águas Claras, Almécega e Verde serem consideradas oligotróficas e a lagoa Carioca meso-oligotrófica. / Benthic macroinvertebrates are important components of aquatic ecosystems due to their role in the energy flow and material cycling. They have gradually received more attention in ecological studies in the last decades. The present study aimed a comparative limnological characterization of four lakes belonging to the middle Rio Doce Valley lacustrine system, MG (Águas Claras, Almécega, Verde and Carioca lakes), and the study of its benthic macroinvertebrate communities with emphasis on the taxonomical composition, spatial and temporal distribution and diversity, besides an evaluation of possible relationships with the occurrence of exotic species in the system. The lakes are located in the interplanaltic depression of Rio Doce Valley, an extense drainage web surrounded by Atlantic Forest remnants (19 'DEGREES' 45’ 25,7" and 19 'DEGREES' 53’ 11,6" South; 42 'DEGREES' 37’ 35,6" and 42 'DEGREES' 35’ 11,3" West). Samplings for physical, chemical and biological analyses were carried out in September and December 2002 and in March and June 2003. Sediment sampling for granulometric determinations and for benthic community analyses were performed with a Van Veen (337 'CM POT.2') dredge. Considering the four lakes and the sampling seasons, 77 stations were sampled. A total of 56 taxa were identified, 2 belonging to the Mollusca, Gastropoda; 13 to Oligochaeta and 1 to the Hirudinae, Annelida; 1 to Nematoda and 41 Insecta, Arthropoda. Among the Insecta 27 taxa belonged to the family Chironomidae. The highest richness of taxa was recorded in lake Carioca (43 taxa) and the lowest in lake Águas Claras (27 taxa). Melanoides tuberculata, an invader molusc was the numerically dominant taxon in Águas Claras and Almécega lakes. In lake Verde this species ocurred in densities 5 times lower than in those lakes where its populations are already well established. This mollusc does not occur in lake Carioca. This was among the lakes studied, the one where the highjest richness of taxa was recorded and Chironomidae were the most representative benthic macroinvertebrates. There were seasonal changes in the population densities. There are also diferences regarding the taxonomic composition of the benthic community among the littoral and the limnetic regions evidencing the system compartimentalization. The sediments of lake Águas Claras, Almécega and Verde have low organic matter content in the littoral region, being classified as mineral and sandy, whereas the sediment of lake Carioca is loamy and organic. Regarding the general limnological conditions the results indicate that lake waters are slightly acidic and well oxygenated. Nutrient concentrations in the water column are relatively low. The lakes Águas Claras, Almécega and Verde can be classified as oligotrophic and lake Carioca as meso-oligotrophic.