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<p><a href="" target="_blank">Synthetic microbial communities (SynComs) are an important focus in modern microbiology. SynComs are used for studying the dynamics of naturally occurring microbial communities ranging from soil to the human gut. Synthetic refers to the assemblage of some or all the members of these communities in a laboratory setting. SynComs allow for communities difficult to study <i>in situ</i> to be studied in a controlled environment, or they may be used to create beneficial products like biofertilizers. When SynComs are used as products, the focus shifts to optimizing a desired outcome of a culture. For biofertilizers, a high diversity is key to producing a functionally redundant product for stimulating plant growth. Media manipulation is a common approach for inducing community changes in a SynCom. Amino acids (AA) are a media supplement that soil microbes (often the components of biofertilizers) are particularly fond of to support their metabolic activities. This study took a scale-up approach to assess the changes in growth dynamics of a SynCom (Environoc© 401) when supplemented with different concentrations of commercially available AA products from plant and animal sources. Expanding from microplates, to shake flasks, then into a 4L bioreactor, Environoc© 401 cultures were compared for their maximum growth rate, time in lag phase, and final growth (optical density or viable cell density) when supplemented with these AA products at various concentrations. Furthermore, Illumina sequencing of the 16S rRNA gene was used to evaluate community-level changes from these treatments based on taxonomic, alpha (Chao 1 and Shannon indices), and beta diversity (Generalized UniFrac) of shake flask and bioreactor samples. Quantitative PCR was also used to assess the relative change of three select species of the SynCom in each AA treatment. Shake flask data revealed significant changes in the growth dynamics of the SynComs within AA treatment groups. Whether the AA was animal or plant derived, generally as the concentration of AA increased, the maximum growth rate decreased, lag time increased, and final growth readings increased. The best AA supplement and rate according to the growth metrics and <i>Curveball </i>analysis was Stimtide at a 33% supplementation rate. This was compared with the control at the bioreactor scale where it showed higher overall final growth and a higher taxonomic and alpha diversity. The scale-up approach to this study was successful at selecting the best amino acid supplement type and rate despite having less sophisticated control and monitoring compared to larger scales (i.e. the bioreactor). Use of the <i>Curveball</i> modeling program was useful for treatment group selection but did not always predict the outcomes seen in the live cultures. The use of AA as a media supplement can increase growth and diversity of a SynCom, though not all AA supplements or rates affect growth and community dynamics in the same way</a>.</p>

A ciclagem de matéria orgânica (MO) no ambiente marinho é um processo-chave para o ciclo global de carbono. Os sedimentos costeiros são de suma importância para a ciclagem de carbono pois atuam como receptores de grandes quantidades de MO alóctone (i.e. terrestre) e autóctone (i.e. marinho). A miríade dos componentes orgânicos e suas diferentes características dificultam o entendimento das fontes de MO em ambientes costeiros. Este trabalho visou entender a origem e a composição da MO (através de biomarcadores lipídicos) e a dinâmica da comunidade microbiana (método ATP) em sedimentos superficiais de diferentes ecossistemas marinhos da costa sudeste do Brasil: (i) margem continental de Cabo Frio; (ii) sistema lagunar de Saquarema; (iii) áreas costeiras e a plataforma continental de Ubatuba; (iv) e a plataforma adjacente ao estuário de Santos. Os resultados apontaram uma origem predominantemente autóctone para a MO nestes sistemas, com contribuição terrestre reduzida e limitada à áreas próximas à costa. Processos oceanográficos e forçantes ambientais são cruciais para a composição da MO sedimentar e são discutidas para cada um dos ecossistemas estudados. / The cycling of the organic matter (OM) in the marine environment is a key process in the global carbon cycle. Coastal sediments are important to the global carbon cycle, since they receive large inputs from both marine and terrestrial OM. The myriad of organic compounds and their spectrum of reactivity complicate the understanding of OM sources in coastal environments. In this work, we aimed to access the origin and composition of the OM (through lipid biomarkers) and the microbial dynamics (ATP method) in surface sediments of diverse marine ecosystems from the SE Brazilian coast: (i) the continental margin off Cabo Frio; (ii) the lagoonal system of Saquarema; (iii) coastal and shelf areas from Ubatuba; and (iv) the continental shelf adjacent to Santos estuary. The results showed a dominance of autochthonous OM, with a minor fraction of the OM derived from terrestrial sources and restricted to areas close to the coast. Oceanographic processes and environmental forces are crucial to the composition of sedimentary OM and are discussed for each of those ecosystems.

Soil is an important ecosystem that supports a wide variety of organisms such as bacteria, fungi, arthropods and nematodes. This sensitive ecosystem may be influenced by various factors, including agricultural management practices. With the introduction of genetically modified (GM) glyphosate-tolerant (RoundUp ® Ready: RR) crops, herbicides such as glyphosate have been increasingly used. However, little is known about the effect of glyphosate on the biological communities in these herbicide-sprayed soils. With the intimate proximity that microorganisms and nematodes have with the roots of plants, these organisms can be used to assess changes that may occur in the soil surrounding roots of RR crops. The aim of this study was to determine microbial community structure and nematode diversity, with emphasis on that of non-parasitic nematodes, in soil samples from conventional soybean (CS) - and RR- soybean fields compared to that in adjacent natural veld (NV) areas. Samples were collected from twenty three sites at six localities that are situated within the soybean-production areas of South Africa. These sites represented fields where RR and CS soybean grew, as well as surrounding NV. All RR fields have been treated with glyphosate for no less than five years. Microbial community structures of the twenty three sites in the RR, CS and NV ecosystems were determined by phospholipid fatty acid (PLFA) analyses. Nematode diversity was determined by extracting the nematodes from soil samples and conducting a faunal analysis. Soil physical and chemical properties were determined by an independent laboratory, Eco-Analytica (North West University, Potchefstroom) according to standard procedures. Results from this study indicated differences in microbial community structure between the various localities. However, there were no significant (p ≤ 0.05) differences in microbial community structures between RR- and CS ecosystems. Soils of both RR- and CS crops were primarily dominated by bacteria. Nematode identification and faunal analysis also indicated no significant (p ≤ 0.05) differences between the different non-parasitic/beneficial nematodes that were present in soils of these two ecosystems during the time of sampling. Non-parasitic nematode communities were primarily dominated by bacterivores. A faunal analysis indicated that most of the sites contained enriched, but unstructured soil food-webs. However, four of the sites showed enriched and structured food webs due to the presence of non-parasitic nematodes with high coloniser-persister (cp) values. Relationships between non-parasitic nematode – and microbial communities showed that there was a positive relationship between nematode functional groups and their corresponding microbial prey. From the results obtained in this study, it can be concluded that the community structures of both non-parasitic nematodes and microorganisms shared similarities. These community structures showed no long-term detrimental effects of glyphosate application in the soils surrounding roots of RR soybean crops. Relationships existed between non-parasitic nematode and microbial communities in the rhizosphere of soybean crops and natural veld. For example, bacterivore nematodes had a strong positive relationship with gram-negative bacteria. Similar but weaker relationships also existed between carnivores, omnivores, plantparasitic nematodes and gram-negative bacteria. A positive relationship also existed between fungivores and fungal fatty acids. This emphasises the value of these organisms as indicators of soil health and also the impact that agricultural practices can have on soils. / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2014

Soil is an important ecosystem that supports a wide variety of organisms such as bacteria, fungi, arthropods and nematodes. This sensitive ecosystem may be influenced by various factors, including agricultural management practices. With the introduction of genetically modified (GM) glyphosate-tolerant (RoundUp ® Ready: RR) crops, herbicides such as glyphosate have been increasingly used. However, little is known about the effect of glyphosate on the biological communities in these herbicide-sprayed soils. With the intimate proximity that microorganisms and nematodes have with the roots of plants, these organisms can be used to assess changes that may occur in the soil surrounding roots of RR crops. The aim of this study was to determine microbial community structure and nematode diversity, with emphasis on that of non-parasitic nematodes, in soil samples from conventional soybean (CS) - and RR- soybean fields compared to that in adjacent natural veld (NV) areas. Samples were collected from twenty three sites at six localities that are situated within the soybean-production areas of South Africa. These sites represented fields where RR and CS soybean grew, as well as surrounding NV. All RR fields have been treated with glyphosate for no less than five years. Microbial community structures of the twenty three sites in the RR, CS and NV ecosystems were determined by phospholipid fatty acid (PLFA) analyses. Nematode diversity was determined by extracting the nematodes from soil samples and conducting a faunal analysis. Soil physical and chemical properties were determined by an independent laboratory, Eco-Analytica (North West University, Potchefstroom) according to standard procedures. Results from this study indicated differences in microbial community structure between the various localities. However, there were no significant (p ≤ 0.05) differences in microbial community structures between RR- and CS ecosystems. Soils of both RR- and CS crops were primarily dominated by bacteria. Nematode identification and faunal analysis also indicated no significant (p ≤ 0.05) differences between the different non-parasitic/beneficial nematodes that were present in soils of these two ecosystems during the time of sampling. Non-parasitic nematode communities were primarily dominated by bacterivores. A faunal analysis indicated that most of the sites contained enriched, but unstructured soil food-webs. However, four of the sites showed enriched and structured food webs due to the presence of non-parasitic nematodes with high coloniser-persister (cp) values. Relationships between non-parasitic nematode – and microbial communities showed that there was a positive relationship between nematode functional groups and their corresponding microbial prey. From the results obtained in this study, it can be concluded that the community structures of both non-parasitic nematodes and microorganisms shared similarities. These community structures showed no long-term detrimental effects of glyphosate application in the soils surrounding roots of RR soybean crops. Relationships existed between non-parasitic nematode and microbial communities in the rhizosphere of soybean crops and natural veld. For example, bacterivore nematodes had a strong positive relationship with gram-negative bacteria. Similar but weaker relationships also existed between carnivores, omnivores, plantparasitic nematodes and gram-negative bacteria. A positive relationship also existed between fungivores and fungal fatty acids. This emphasises the value of these organisms as indicators of soil health and also the impact that agricultural practices can have on soils. / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2014

Dans les environnements côtiers, soumis à l’impact des marées noires, les microorganismes jouent un rôle crucial dans le devenir des hydrocarbures pétroliers. Toutefois, de nombreux facteurs influencent les activités microbiennes, notamment par les organismes bioturbateurs qui modifient la pénétration de l’oxygène dans les sédiments. Le travail de la thèse vise à mieux comprendre l’impact d’une pollution pétrolière sur les communautés microbiennes dans des sédiments bio turbés. Il s’agissait de comparer les remaniements structuraux de la communauté microbienne liée à la contamination pétrolière dans des sédiments présentant une faible et une forte activité de bioturbation. Des sédiments marins ont été maintenus en microcosmes durant 9 mois et soumis à quatre conditions : (i) pas de traitement (contrôle), (ii) pétrole, (iii) bioturbation et (iv) pétrole et bioturbation. Les efficacités de dégradation des hydrocarbures pétroliers se sont révélées similaires dans les deux types de sédiments. Par des approches moléculaires, la diversité taxonomique et fonctionnelle des communautés microbiennes totales et métaboliquement actives a été évaluée au cours du temps. Les communautés microbiennes ont subi d’importants remaniements structuraux spécifiques à chaque traitement. Nous suggérons que le fonctionnement global de la communauté est modifié par l’activité bioturbatrice sans pour autant modifier l’activité de dégradation. Ces travaux ont mis en évidence une redondance fonctionnelle de l’activité de biodégradation des hydrocarbures pétroliers des communautés microbiennes. L’isolement de communautés hydrocarbonoclastes a permis de confirmer cette redondance fonctionnelle. / Coastal areas such as mudflats are affected by oil spills. In these environments, microorganisms play a crucial role in the fate of petroleum hydrocarbons. However, many factors influence microbial activities, especially the bioturbating organisms, which altered the oxygen penetration in sediments. The present work attempts to better understand the impact of petroleum contamination on microbial community associated with petroleum contamination in sediments with low and high bioturbation activity. This study is based on microcosm experiments with a device simulating tidal cycles. Marine sediments were maintained for 9 months in microcosms and subjected to four conditions: (i) no treatment (control), (ii) oil, (iii) bioturbation and (iv) oil and bioturbation. Chemical, microbiological and biological analyses were conducted throughout the experiment. The efficiencies of degradation of petroleum hydrocarbons were similar in both sediments. By molecular approaches, we assessed the dynamic of the functional and taxonomic diversity of the total and metabolically active communities during the oil contamination. Microbial communities showed significant structural rearrangements specific for each treatment that resulted in distinct microbial communities in both sediments. Hence, the overall microbial community structure was changed by bioturbating activity without changing the degradation capacity revealing a functional redundancy of the biodegradation capacity of hydrocarbons. This result was further supported by the isolation and characterization of hydro carbonoclastic communities.

A ciclagem de matéria orgânica (MO) no ambiente marinho é um processo-chave para o ciclo global de carbono. Os sedimentos costeiros são de suma importância para a ciclagem de carbono pois atuam como receptores de grandes quantidades de MO alóctone (i.e. terrestre) e autóctone (i.e. marinho). A miríade dos componentes orgânicos e suas diferentes características dificultam o entendimento das fontes de MO em ambientes costeiros. Este trabalho visou entender a origem e a composição da MO (através de biomarcadores lipídicos) e a dinâmica da comunidade microbiana (método ATP) em sedimentos superficiais de diferentes ecossistemas marinhos da costa sudeste do Brasil: (i) margem continental de Cabo Frio; (ii) sistema lagunar de Saquarema; (iii) áreas costeiras e a plataforma continental de Ubatuba; (iv) e a plataforma adjacente ao estuário de Santos. Os resultados apontaram uma origem predominantemente autóctone para a MO nestes sistemas, com contribuição terrestre reduzida e limitada à áreas próximas à costa. Processos oceanográficos e forçantes ambientais são cruciais para a composição da MO sedimentar e são discutidas para cada um dos ecossistemas estudados. / The cycling of the organic matter (OM) in the marine environment is a key process in the global carbon cycle. Coastal sediments are important to the global carbon cycle, since they receive large inputs from both marine and terrestrial OM. The myriad of organic compounds and their spectrum of reactivity complicate the understanding of OM sources in coastal environments. In this work, we aimed to access the origin and composition of the OM (through lipid biomarkers) and the microbial dynamics (ATP method) in surface sediments of diverse marine ecosystems from the SE Brazilian coast: (i) the continental margin off Cabo Frio; (ii) the lagoonal system of Saquarema; (iii) coastal and shelf areas from Ubatuba; and (iv) the continental shelf adjacent to Santos estuary. The results showed a dominance of autochthonous OM, with a minor fraction of the OM derived from terrestrial sources and restricted to areas close to the coast. Oceanographic processes and environmental forces are crucial to the composition of sedimentary OM and are discussed for each of those ecosystems.